• Manuals

Browse the manual

  • Introduction to Biomedical Genomics Workbench
    • Contact information
      • System requirements
        • Limitations on maximum number of cores
        • Workbench Licenses
          • Request an evaluation license
            • Download a license using a license order ID
              • Import a license from a file
                • Upgrade license
                  • Configure license server connection
                    • Download a static license on a non-networked machine
                      • Limited mode
                      • About CLC Workbenches
                        • New program feature request
                          • Getting help
                          • When the program is installed: Getting started
                            • Import of example data
                            • Plugins
                              • Installing plugins
                                • Uninstalling plugins
                                  • Updating plugins
                                    • Resources
                                    • Network configuration
                                    • User interface
                                      • View Area
                                        • Open view
                                          • Show element in another view
                                            • Close views
                                              • Save changes in a view
                                                • Undo/Redo
                                                  • Arrange views in View Area
                                                    • Moving a view to a different screen
                                                      • Side Panel
                                                      • Zoom and selection in View Area
                                                        • Zoom in
                                                          • Zoom out
                                                            • Selecting, panning and zooming
                                                            • Toolbox and Status Bar
                                                              • Processes
                                                                • Toolbox
                                                                  • Status Bar
                                                                  • Workspace
                                                                    • Create Workspace
                                                                      • Select Workspace
                                                                        • Delete Workspace
                                                                        • List of shortcuts
                                                                        • Data organization
                                                                          • Navigation Area
                                                                            • Data structure
                                                                              • Create new folders
                                                                                • Sorting folders
                                                                                  • Multiselecting elements
                                                                                    • Moving and copying elements
                                                                                      • Change element names
                                                                                        • Delete, restore and remove elements
                                                                                          • Show folder elements in a table
                                                                                          • Metadata
                                                                                            • Setting up Metadata Tables
                                                                                              • Editing the metadata structure
                                                                                                • Importing metadata columns
                                                                                                  • Editing metadata rows
                                                                                                    • Importing metadata rows
                                                                                                      • Associating data elements with metadata
                                                                                                        • Finding data elements based on metadata
                                                                                                          • Viewing metadata associations
                                                                                                            • Exporting metadata
                                                                                                            • Customized attributes on data locations
                                                                                                              • Configuring which fields should be available
                                                                                                                • Editing lists
                                                                                                                  • Removing attributes
                                                                                                                    • Changing the order of the attributes
                                                                                                                    • Filling in values
                                                                                                                      • What happens when a clc object is copied to another data location?
                                                                                                                        • Searching
                                                                                                                        • Local search
                                                                                                                          • What kind of information can be searched?
                                                                                                                            • Quick search
                                                                                                                              • Advanced search
                                                                                                                                • Search index
                                                                                                                                  • Import your own reference data
                                                                                                                                    • Retrieving reference data tracks
                                                                                                                                    • Sequence web info
                                                                                                                                      • Google sequence
                                                                                                                                        • NCBI
                                                                                                                                          • PubMed References
                                                                                                                                            • UniProt
                                                                                                                                              • Additional annotation information
                                                                                                                                            • User preferences and settings
                                                                                                                                              • General preferences
                                                                                                                                                • Default view preferences
                                                                                                                                                  • Number formatting in tables
                                                                                                                                                    • Import and export Side Panel settings
                                                                                                                                                    • Data preferences
                                                                                                                                                      • Advanced preferences
                                                                                                                                                        • Default data location
                                                                                                                                                        • Export/import of preferences
                                                                                                                                                          • The different options for export and import
                                                                                                                                                          • View settings for the Side Panel
                                                                                                                                                            • Saving, removing and applying saved settings
                                                                                                                                                          • Printing
                                                                                                                                                            • Selecting which part of the view to print
                                                                                                                                                              • Page setup
                                                                                                                                                                • Header and footer
                                                                                                                                                                • Print preview
                                                                                                                                                                • Import/export of data and graphics
                                                                                                                                                                  • Standard import
                                                                                                                                                                    • Import using the import dialog
                                                                                                                                                                      • Import using drag and drop
                                                                                                                                                                        • Import using copy/paste of text
                                                                                                                                                                          • External files
                                                                                                                                                                          • Import tracks
                                                                                                                                                                            • Import high-throughput sequencing data
                                                                                                                                                                              • 454 from Roche Applied Science
                                                                                                                                                                                • Illumina
                                                                                                                                                                                  • PacBio
                                                                                                                                                                                    • SOLiD from Life Technologies
                                                                                                                                                                                      • Fasta read files
                                                                                                                                                                                        • Sanger sequencing data
                                                                                                                                                                                          • Ion Torrent PGM from Life Technologies
                                                                                                                                                                                            • Complete Genomics
                                                                                                                                                                                              • General notes on handling paired data
                                                                                                                                                                                                • SAM and BAM mapping files
                                                                                                                                                                                                • Import Primer Pairs
                                                                                                                                                                                                  • Data export
                                                                                                                                                                                                    • Export of folders and multiple elements in CLC format
                                                                                                                                                                                                      • Export of dependent elements
                                                                                                                                                                                                        • Export history
                                                                                                                                                                                                          • The CLC format
                                                                                                                                                                                                            • Backing up data from the CLC Workbench
                                                                                                                                                                                                              • Export of workflow output
                                                                                                                                                                                                                • Export of tables
                                                                                                                                                                                                                • Export graphics to files
                                                                                                                                                                                                                  • Which part of the view to export
                                                                                                                                                                                                                    • Save location and file formats
                                                                                                                                                                                                                      • Graphics export parameters
                                                                                                                                                                                                                        • Exporting protein reports
                                                                                                                                                                                                                        • Export graph data points to a file
                                                                                                                                                                                                                          • Copy/paste view output
                                                                                                                                                                                                                          • History log
                                                                                                                                                                                                                            • Element history
                                                                                                                                                                                                                              • Sharing data with history
                                                                                                                                                                                                                            • Batching and result handling
                                                                                                                                                                                                                              • Batch processing
                                                                                                                                                                                                                                • Batch overview
                                                                                                                                                                                                                                  • Batch filtering and counting
                                                                                                                                                                                                                                    • Setting parameters for batch runs
                                                                                                                                                                                                                                      • Running the analysis and organizing the results
                                                                                                                                                                                                                                      • How to handle results of analyses
                                                                                                                                                                                                                                        • Table outputs
                                                                                                                                                                                                                                          • Batch log
                                                                                                                                                                                                                                          • Working with tables
                                                                                                                                                                                                                                            • Filtering tables
                                                                                                                                                                                                                                          • Viewing and editing sequences
                                                                                                                                                                                                                                            • View sequence
                                                                                                                                                                                                                                              • Sequence settings in Side Panel
                                                                                                                                                                                                                                                • Dynamic motifs
                                                                                                                                                                                                                                                  • Restriction sites in the Side Panel
                                                                                                                                                                                                                                                    • Selecting parts of the sequence
                                                                                                                                                                                                                                                      • Editing the sequence
                                                                                                                                                                                                                                                        • Sequence region types
                                                                                                                                                                                                                                                        • Circular DNA
                                                                                                                                                                                                                                                          • Using split views to see details of the circular molecule
                                                                                                                                                                                                                                                            • Mark molecule as circular and specify starting point
                                                                                                                                                                                                                                                            • Working with annotations
                                                                                                                                                                                                                                                              • Viewing annotations
                                                                                                                                                                                                                                                                • Adding annotations
                                                                                                                                                                                                                                                                  • Edit annotations
                                                                                                                                                                                                                                                                    • Removing annotations
                                                                                                                                                                                                                                                                    • Element information
                                                                                                                                                                                                                                                                      • View as text
                                                                                                                                                                                                                                                                        • Sequence Lists
                                                                                                                                                                                                                                                                          • Graphical view of sequence lists
                                                                                                                                                                                                                                                                            • Sequence list table
                                                                                                                                                                                                                                                                              • Extract sequences from sequence list
                                                                                                                                                                                                                                                                            • Viewing structures
                                                                                                                                                                                                                                                                              • Importing molecule structure files
                                                                                                                                                                                                                                                                                • Import issues
                                                                                                                                                                                                                                                                                • Viewing molecular structures in 3D
                                                                                                                                                                                                                                                                                  • Moving and rotating
                                                                                                                                                                                                                                                                                    • Troubleshooting 3D graphics errors
                                                                                                                                                                                                                                                                                    • Customizing the visualization
                                                                                                                                                                                                                                                                                      • Visualization styles and colors
                                                                                                                                                                                                                                                                                        • Project settings
                                                                                                                                                                                                                                                                                        • Snapshots of the molecule visualization
                                                                                                                                                                                                                                                                                          • Tools for linking sequence and structure
                                                                                                                                                                                                                                                                                            • Show sequence associated with molecule
                                                                                                                                                                                                                                                                                              • Link sequence or sequence alignment to structure
                                                                                                                                                                                                                                                                                                • Transfer annotations between sequence and structure
                                                                                                                                                                                                                                                                                                • Protein structure alignment
                                                                                                                                                                                                                                                                                                  • The Align Protein Structure dialog box
                                                                                                                                                                                                                                                                                                    • Example: alignment of calmodulin
                                                                                                                                                                                                                                                                                                      • The Align Protein Structure algorithm
                                                                                                                                                                                                                                                                                                    • Ready-to-Use Workflows descriptions and guidelines
                                                                                                                                                                                                                                                                                                      • General Workflow
                                                                                                                                                                                                                                                                                                        • Somatic Cancer
                                                                                                                                                                                                                                                                                                          • Hereditary Disease
                                                                                                                                                                                                                                                                                                          • Getting started
                                                                                                                                                                                                                                                                                                            • Reference data
                                                                                                                                                                                                                                                                                                              • The Workbench Reference data location
                                                                                                                                                                                                                                                                                                                • Space requirements
                                                                                                                                                                                                                                                                                                                  • Where reference data is downloaded from
                                                                                                                                                                                                                                                                                                                    • Download and configure reference data
                                                                                                                                                                                                                                                                                                                      • Troubleshooting reference data downloads
                                                                                                                                                                                                                                                                                                                      • Create new folder
                                                                                                                                                                                                                                                                                                                        • Import sequencing data
                                                                                                                                                                                                                                                                                                                          • How to import data
                                                                                                                                                                                                                                                                                                                          • Prepare sequencing data
                                                                                                                                                                                                                                                                                                                            • Choosing between Prepare Raw Data and Prepare Overlapping Raw Data workflows
                                                                                                                                                                                                                                                                                                                              • Import adapter trim list
                                                                                                                                                                                                                                                                                                                                • How to run the Prepare Overlapping Raw Data ready-to-use workflow
                                                                                                                                                                                                                                                                                                                                  • How to run the Prepare Raw Data ready-to-use workflow
                                                                                                                                                                                                                                                                                                                                    • Output from the Prepare Overlapping Raw Data and Prepare Raw Data workflows
                                                                                                                                                                                                                                                                                                                                      • How to check the output reports
                                                                                                                                                                                                                                                                                                                                    • Whole genome sequencing (WGS)
                                                                                                                                                                                                                                                                                                                                      • General Workflows (WGS)
                                                                                                                                                                                                                                                                                                                                        • Annotate Variants (WGS)
                                                                                                                                                                                                                                                                                                                                          • Identify Known Variants in One Sample (WGS)
                                                                                                                                                                                                                                                                                                                                          • Somatic Cancer (WGS)
                                                                                                                                                                                                                                                                                                                                            • Filter Somatic Variants (WGS)
                                                                                                                                                                                                                                                                                                                                              • Identify Somatic Variants from Tumor Normal Pair (WGS)
                                                                                                                                                                                                                                                                                                                                                • Identify Variants (WGS)
                                                                                                                                                                                                                                                                                                                                                • Hereditary Disease (WGS)
                                                                                                                                                                                                                                                                                                                                                  • Filter Causal Variants (WGS-HD)
                                                                                                                                                                                                                                                                                                                                                    • Identify Causal Inherited Variants in Family of Four (WGS)
                                                                                                                                                                                                                                                                                                                                                      • Identify Causal Inherited Variants in Trio (WGS)
                                                                                                                                                                                                                                                                                                                                                        • Identify Rare Disease Causing Mutations in Family of Four (WGS)
                                                                                                                                                                                                                                                                                                                                                          • Identify Rare Disease Causing Mutations in Trio (WGS)
                                                                                                                                                                                                                                                                                                                                                            • Identify Variants (WGS-HD)
                                                                                                                                                                                                                                                                                                                                                          • Whole exome sequencing (WES)
                                                                                                                                                                                                                                                                                                                                                            • General Workflows (WES)
                                                                                                                                                                                                                                                                                                                                                              • Annotate Variants (WES)
                                                                                                                                                                                                                                                                                                                                                                • Identify Known Variants in One Sample (WES)
                                                                                                                                                                                                                                                                                                                                                                • Somatic Cancer (WES)
                                                                                                                                                                                                                                                                                                                                                                  • Filter Somatic Variants (WES)
                                                                                                                                                                                                                                                                                                                                                                    • Identify Somatic Variants from Tumor Normal Pair (WES)
                                                                                                                                                                                                                                                                                                                                                                      • Identify Variants (WES)
                                                                                                                                                                                                                                                                                                                                                                        • Identify and Annotate Variants (WES)
                                                                                                                                                                                                                                                                                                                                                                        • Hereditary Disease (WES)
                                                                                                                                                                                                                                                                                                                                                                          • Filter Causal Variants (WES-HD)
                                                                                                                                                                                                                                                                                                                                                                            • Identify Causal Inherited Variants in Family of Four (WES)
                                                                                                                                                                                                                                                                                                                                                                              • Identify Causal Inherited Variants in Trio (WES)
                                                                                                                                                                                                                                                                                                                                                                                • Identify Rare Disease Causing Mutations in Family of Four (WES)
                                                                                                                                                                                                                                                                                                                                                                                  • Identify Rare Disease Causing Mutations in Trio (WES)
                                                                                                                                                                                                                                                                                                                                                                                    • Identify Variants (WES-HD)
                                                                                                                                                                                                                                                                                                                                                                                      • Identify and Annotate Variants (WES-HD)
                                                                                                                                                                                                                                                                                                                                                                                    • Targeted amplicon sequencing (TAS)
                                                                                                                                                                                                                                                                                                                                                                                      • General Workflows (TAS)
                                                                                                                                                                                                                                                                                                                                                                                        • Annotate Variants (TAS)
                                                                                                                                                                                                                                                                                                                                                                                          • Identify Known Variants in One Sample (TAS)
                                                                                                                                                                                                                                                                                                                                                                                          • Somatic Cancer (TAS)
                                                                                                                                                                                                                                                                                                                                                                                            • Filter Somatic Variants (TAS)
                                                                                                                                                                                                                                                                                                                                                                                              • Identify Somatic Variants from Tumor Normal Pair (TAS)
                                                                                                                                                                                                                                                                                                                                                                                                • Identify Variants (TAS)
                                                                                                                                                                                                                                                                                                                                                                                                  • Identify and Annotate Variants (TAS)
                                                                                                                                                                                                                                                                                                                                                                                                  • Hereditary Disease (TAS)
                                                                                                                                                                                                                                                                                                                                                                                                    • Filter Causal Variants (TAS-HD)
                                                                                                                                                                                                                                                                                                                                                                                                      • Identify Causal Inherited Variants in Family of Four (TAS)
                                                                                                                                                                                                                                                                                                                                                                                                        • Identify Causal Inherited Variants in Trio (TAS)
                                                                                                                                                                                                                                                                                                                                                                                                          • Identify Rare Disease Causing Mutations in Family of Four (TAS)
                                                                                                                                                                                                                                                                                                                                                                                                            • Identify Rare Disease Causing Mutations in Trio (TAS)
                                                                                                                                                                                                                                                                                                                                                                                                              • Identify Variants (TAS-HD)
                                                                                                                                                                                                                                                                                                                                                                                                                • Identify and Annotate Variants (TAS-HD)
                                                                                                                                                                                                                                                                                                                                                                                                              • Whole Transcriptome Sequencing (WTS)
                                                                                                                                                                                                                                                                                                                                                                                                                • Analysis of multiple samples
                                                                                                                                                                                                                                                                                                                                                                                                                  • Annotate Variants (WTS)
                                                                                                                                                                                                                                                                                                                                                                                                                    • Compare variants in DNA and RNA
                                                                                                                                                                                                                                                                                                                                                                                                                      • Identify Candidate Variants and Genes from Tumor Normal Pair
                                                                                                                                                                                                                                                                                                                                                                                                                        • Identify variants and add expression values
                                                                                                                                                                                                                                                                                                                                                                                                                          • Identify and Annotate Differentially Expressed Genes and Pathways
                                                                                                                                                                                                                                                                                                                                                                                                                          • Using data from other workbenches
                                                                                                                                                                                                                                                                                                                                                                                                                            • Open outputs from other workbenches
                                                                                                                                                                                                                                                                                                                                                                                                                            • Genome browser tools
                                                                                                                                                                                                                                                                                                                                                                                                                              • Create new genome browser view
                                                                                                                                                                                                                                                                                                                                                                                                                                • Genome browser view
                                                                                                                                                                                                                                                                                                                                                                                                                                  • Adding ideogram to Genome Browser View
                                                                                                                                                                                                                                                                                                                                                                                                                                    • Zooming and navigating the genome browser views
                                                                                                                                                                                                                                                                                                                                                                                                                                      • Adding, removing and reordering tracks
                                                                                                                                                                                                                                                                                                                                                                                                                                        • Showing a track in a table
                                                                                                                                                                                                                                                                                                                                                                                                                                          • Open track from a track list in table view
                                                                                                                                                                                                                                                                                                                                                                                                                                            • Finding annotations on the genome
                                                                                                                                                                                                                                                                                                                                                                                                                                              • Extract sequences from tracks
                                                                                                                                                                                                                                                                                                                                                                                                                                                • Creating track lists in workflows
                                                                                                                                                                                                                                                                                                                                                                                                                                                • Creating graph tracks
                                                                                                                                                                                                                                                                                                                                                                                                                                                • Quality control tools
                                                                                                                                                                                                                                                                                                                                                                                                                                                  • QC for Target Sequencing
                                                                                                                                                                                                                                                                                                                                                                                                                                                    • Running the 'QC for Target Sequencing' tool
                                                                                                                                                                                                                                                                                                                                                                                                                                                      • Coverage summary report
                                                                                                                                                                                                                                                                                                                                                                                                                                                        • Per-region statistics
                                                                                                                                                                                                                                                                                                                                                                                                                                                          • Coverage table
                                                                                                                                                                                                                                                                                                                                                                                                                                                            • Coverage graph
                                                                                                                                                                                                                                                                                                                                                                                                                                                            • QC for Sequencing Reads
                                                                                                                                                                                                                                                                                                                                                                                                                                                              • Report content
                                                                                                                                                                                                                                                                                                                                                                                                                                                                • Adapters
                                                                                                                                                                                                                                                                                                                                                                                                                                                                  • Running the 'QC for Sequencing Reads' tool
                                                                                                                                                                                                                                                                                                                                                                                                                                                                  • QC for Read Mapping
                                                                                                                                                                                                                                                                                                                                                                                                                                                                    • Running the 'QC for Read Mapping' tool
                                                                                                                                                                                                                                                                                                                                                                                                                                                                      • Summary mapping report
                                                                                                                                                                                                                                                                                                                                                                                                                                                                    • Preparing raw data tools
                                                                                                                                                                                                                                                                                                                                                                                                                                                                      • Merge overlapping pairs
                                                                                                                                                                                                                                                                                                                                                                                                                                                                        • Using quality scores when merging
                                                                                                                                                                                                                                                                                                                                                                                                                                                                          • Report of merged pairs
                                                                                                                                                                                                                                                                                                                                                                                                                                                                          • Trim Sequences
                                                                                                                                                                                                                                                                                                                                                                                                                                                                            • Quality trimming
                                                                                                                                                                                                                                                                                                                                                                                                                                                                              • Adapter trimming
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                • Length trimming
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  • Trim output
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  • Demultiplex reads
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  • Resequencing analysis tools
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    • Identify Known Mutations from Sample Mappings
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      • Input and Parameters
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        • Output from the 'Identify Known Mutations from Sample Mappings' tool
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          • How to run the 'Identify Known Mutations from Sample Mappings' tool
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          • Trim primers of mapped reads
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            • Extract reads based on overlap
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              • Map Reads to Reference
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                • Selecting reads and reference
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  • Including or excluding regions (masking)
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    • Mapping parameters
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      • Mapping paired reads
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        • Non-specific matches
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          • Gap placement
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            • Computational requirements
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              • Reference Caching
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              • Mapping output options
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                • Color space
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  • Sequencing
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    • Error modes
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      • Mapping in color space
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        • Viewing color space information
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        • Mapping result
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          • View settings in the Side Panel
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          • Local realignment
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            • Method
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              • Realignment of unaligned ends
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                • Guided Realignment
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  • Multi-pass local realignment
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    • Known Limitations
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      • Computational Requirements
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        • How to run the Local Realignment tool
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        • Merge mapping results
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          • Copy Number Variant Detection
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            • Running the Copy Number Variant Detection tool
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              • Region-level CNV track (Region CNVs)
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                • Target-level CNV track (Target CNVs)
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  • Gene-level annotation track (Gene CNVs)
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    • CNV results report
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      • CNV algorithm report
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      • Remove duplicate mapped reads
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        • Algorithm details and parameters
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          • Running the duplicate reads removal
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          • Coverage analysis
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            • Running the Coverage analysis tool
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            • Variant Detectors - overview
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              • Differences in the variants called by the different tools
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                • How the variant detection tools work
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                • Basic Variant Detection
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  • Fixed Ploidy Variant Detection
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    • Ploidy and sensitivity
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    • Low Frequency Variant Detection
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      • Variant Detectors - error model estimation
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        • Variant Detectors - filters
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          • General filters
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            • Noise filters
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            • Variant Detectors - the outputs
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              • The variant track output
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                • The annotated table output
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  • The report
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  • The Fixed Ploidy and Low Frequency variant callers: detailed descriptions
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    • The Fixed Ploidy Variant Caller: Models and methods
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      • The Low Frequency Variant caller: Models and methods
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      • InDels and Structural Variants
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        • How to run the InDels and Structural Variants tool
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          • The Structural Variants and InDels output
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            • The InDels and Structural Variants detection algorithm
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              • The InDels and Structural Variants detection algorithm - Step 1: Creating Left- and Right breakpoint signatures
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                • The InDels and Structural Variants detection algorithm - Step 2: Creating Structural variant signatures
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  • Theoretically expected structural variant signatures
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    • How sequence complexity is calculated
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    • Variant data
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      • Variant tracks
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        • The annotated variant table
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          • Variant types
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          • Detailed information about overlapping paired reads
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          • Add information to variants tools
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            • Add information from variant databases
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              • Add conservation scores
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                • Add exon number
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  • Add flanking sequence
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    • Add fold changes
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      • Add information about amino acid changes
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        • Add information from genomic regions
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          • Add information from overlapping genes
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            • Link Variants to 3D Protein Structure
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              • Method details
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              • Download 3D Protein Structure Database
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                • From databases
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  • Add information from 1000 Genomes Project
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    • Add information from COSMIC
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      • Add information from ClinVar
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        • Add information from common dbSNP
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          • Add information from HapMap
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            • Add information from dbSNP
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          • Remove variants tools
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            • Remove variants found in external database
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              • Remove variants not found in external database
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                • Remove false positives
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  • Remove Germline Variants
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    • Remove reference variants
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      • Remove variants inside genome regions
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        • Remove variants outside genome regions
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          • Remove variants outside targeted regions
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            • From databases
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              • Remove variants found in 1000 genomes project
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                • Remove variants found in common dbSNP
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  • Remove variants found in HapMap
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                • Add information to genes tool
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  • Add information from overlapping variants
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  • Compare samples tools
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    • Compare shared variants within a group of samples
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      • Identify Enriched Variants in Case vs Control Group
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        • Trio analysis
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        • Identify candidate variants tools
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          • Identify candidate variants
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            • Remove information from variants
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              • Identify variants with effect on splicing
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              • Identify candidate genes tools
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                • Identify differentially expressed gene groups and pathways
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  • Identify highly mutated gene groups and pathways
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    • Identify mutated genes
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      • Select genes by name
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      • Transcriptomics tools
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        • RNA-Seq analysis
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          • Specifying reads and reference
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            • Tightly packed genes and genes in operons
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              • Defining mapping options for RNA-Seq
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                • Calculating expression values from RNA-Seq
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  • Specifying RNA-Seq outputs
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    • Interpreting the RNA-Seq analysis result
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      • Create fold change track
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      • Small RNA analysis
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        • Extract and count
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          • Downloading miRBase
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            • Annotating and merging small RNA samples
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              • Working with the small RNA sample
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                • Exploring novel miRNAs
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                • Experimental design
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  • Setting up an experiment
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    • Organization of the experiment table
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      • Adding annotations to an experiment
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        • Scatter plot view of an experiment
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          • Cross-view selections
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          • Working with tracks and experiments
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            • Data structures for transcriptomics
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              • From Tracks to Experiments
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                • From Experiments to Tracks
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  • Running the Extract Differentially Expressed Genes tool
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    • Interpreting the results of the Extract Differentially Expressed Genes tool
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      • Visualizing RNA-Seq read tracks for the experiment
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      • Transformation and normalization
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        • Selecting transformed and normalized values for analysis
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          • Transformation
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            • Normalization
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            • Quality control
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              • Creating box plots - analyzing distributions
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                • Hierarchical clustering of samples
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  • Principal component analysis
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  • Statistical analysis - identifying differential expression
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    • Empirical analysis of DGE
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      • Tests on proportions
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        • Gaussian-based tests
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          • Corrected p-values
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            • Volcano plots - inspecting the result of the statistical analysis
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            • Feature clustering
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              • Hierarchical clustering of features
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                • K-means/medoids clustering
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                • Annotation tests
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  • Hypergeometric tests on annotations
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    • Gene set enrichment analysis
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    • General plots
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      • Histogram
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        • MA plot
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          • Scatter plot
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        • Helper tools
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          • Extract sequences
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            • Filter Based on Overlap
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            • Cloning and cutting
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              • Molecular cloning
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                • Introduction to the cloning editor
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  • The cloning workflow
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    • Manual cloning
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      • Insert restriction site
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      • Gateway cloning
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        • Add attB sites
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          • Create entry clones (BP)
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            • Create expression clones (LR)
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            • Restriction site analysis
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              • Dynamic restriction sites
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                • Restriction site analysis from the Toolbox
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                • Gel electrophoresis
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  • Separate fragments of sequences on gel
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    • Separate sequences on gel
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      • Gel view
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      • Restriction enzyme lists
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        • Create enzyme list
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          • View and modify enzyme list
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        • Sequencing Data Analysis
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          • Importing and viewing trace data
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            • Scaling traces
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              • Trace settings in the Side Panel
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              • Trim sequences
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                • Trimming using the Trim tool
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  • Manual trimming
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  • Assemble sequences
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    • Sort sequences by name
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      • Assemble sequences to reference
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        • Add sequences to an existing contig
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          • View and edit read mappings
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            • View settings in the Side Panel
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              • Editing the read mapping
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                • Sorting reads
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  • Read conflicts
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    • Extract parts of a mapping
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      • Variance table
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      • Reassemble contig
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        • Secondary peak calling
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        • Primers
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          • Primer design - an introduction
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            • General concept
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              • Scoring primers
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              • Setting parameters for primers and probes
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                • Primer Parameters
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                • Graphical display of primer information
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  • Compact information mode
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    • Detailed information mode
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    • Output from primer design
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      • Saving primers
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        • Saving PCR fragments
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          • Adding primer binding annotation
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          • Standard PCR
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            • User input
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              • Standard PCR output table
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              • Nested PCR
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                • Nested PCR output table
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                • TaqMan
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  • TaqMan output table
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  • Sequencing primers
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    • Sequencing primers output table
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    • Alignment-based primer and probe design
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      • Specific options for alignment-based primer and probe design
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        • Alignment based design of PCR primers
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          • Alignment-based TaqMan probe design
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          • Analyze primer properties
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            • Find binding sites and create fragments
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              • Binding parameters
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                • Results - binding sites and fragments
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                • Order primers
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                • Epigenomics
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  • ChIP-Seq Analysis
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    • Quality Control of ChIP-seq data
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      • Learning peak shapes
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        • Applying peak shape filters to call peaks
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          • Running the Transcription Factor ChIP-Seq tool
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          • Annotate with nearby gene information
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          • Workflows
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            • Creating a workflow
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              • Adding workflow elements
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                • Configuring workflow elements
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  • Locking and unlocking parameters
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    • Connecting workflow elements
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      • Input and output
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        • Layout
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          • Input modifying tools
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            • Workflow validation
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              • Workflow creation helper tools
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                • Adding to workflows
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  • Snippets in workflows
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    • Supported data flows
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    • Distributing and installing workflows
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      • Creating a workflow installation file
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        • Installing a workflow
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          • Workflow identification and versioning
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            • Automatic update of workflow elements
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            • Executing a workflow
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              • Open copy of ready-to-use workflow
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              • Legacy tools
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                • Create Filter Criteria (legacy)
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  • Identify candidate variants (legacy)
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    • Quality-based variant detection
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      • Assessing the quality of the neighborhood bases
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        • Significance of variant
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          • Ploidy and genetic code
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            • Reporting the variants
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            • Probabilistic variant detection
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              • Calculation of the prior and error probabilities
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                • Calculation of the likelihood
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  • Calculation of the posterior probability for each site type at each position in the genome
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    • Comparison with the reference sequence and identification of candidate variants
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      • Posterior filtering and reporting of variants
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        • Running the variant detection
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          • Setting ploidy and genetic code
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            • Reporting the variants found
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          • Appendix
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            • Use of multi-core computers
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              • Reference data overview
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                • Proteolytic cleavage enzymes
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  • Restriction enzymes database configuration
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    • Technical information about modifying Gateway cloning sites
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      • IUPAC codes for amino acids
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        • IUPAC codes for nucleotides
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          • Formats for import and export
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            • List of bioinformatic data formats
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              • List of graphics data formats
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              • SAM/BAM export format specification
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                • Flags
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                • Gene expression annotation files and microarray data formats
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  • GEO (Gene Expression Omnibus)
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    • Affymetrix GeneChip
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      • Illumina BeadChip
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        • Gene ontology annotation files
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          • Generic expression and annotation data file formats
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          • Translation Tables
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            • 1. Standard
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              • 2. Vertebrate Mitochondrial
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                • 3. Yeast Mitochondrial
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  • 4. Mold Mitochondrial; Protozoan Mitochondrial; Coelenterate Mitochondrial; Mycoplasma; Spiroplasma
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    • 5. Invertebrate Mitochondrial
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      • 6. Ciliate Nuclear; Dasycladacean Nuclear; Hexamita Nuclear
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        • 9. Echinoderm Mitochondrial; Flatworm Mitochondrial
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          • 10. Euplotid Nuclear
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            • 11. Bacterial and Plant Plastid
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              • 12. Alternative Yeast Nuclear
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                • 13. Ascidian Mitochondrial
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  • 14. Alternative Flatworm Mitochondrial
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    • 15. Blepharisma Macronuclear
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      • 16. Chlorophycean Mitochondrial
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        • 21. Trematode Mitochondrial
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          • 22. Scenedesmus Obliquus Mitochondrial
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            • 23. Thraustochytrium Mitochondrial
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              • 24. Pterobranchia Mitochondrial
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                • 25. Candidate Division SR1 and Gracilibacteria
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                • Matrices for alignment calculation
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  • PAM30 log-odds matrix
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    • PAM60 log-odds matrix
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      • BLOSUM42 log-odds matrix
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        • BLOSUM62 log-odds matrix
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          • BLOSUM80 log-odds matrix
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        • Bibliography