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• Introduction to Biomedical Genomics Workbench
  • Contact information
  • Download and installation
    • Program download
    • Installation on Microsoft Windows
    • Installation on Mac OS X
    • Installation on Linux with an installer
  • 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
    • Start in safe mode
  • When the program is installed: Getting started
  • Plugins
    • Install
    • Uninstall
    • Updating plugins
  • Network configuration
• User interface
  • View Area
    • Open view
    • History and Info views
    • 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
    • Favorites
    • Status Bar
  • 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
    • Importing Metadata
    • Advanced Metadata Import
    • Associating data elements with metadata
    • Working with data and metadata
  • Working with tables
    • Filtering tables
  • Customized attributes on data locations
    • Filling in values
    • What happens when a clc object is copied to another data location?
    • Searching
  • Local search
    • Quick search
    • Advanced search
• User preferences and settings
  • General preferences
  • View preferences
    • Import and export Side Panel settings
  • Data preferences
  • Advanced preferences
  • Export/import of preferences
  • View settings for the Side Panel
• Printing
  • Selecting which part of the view to print
  • Page setup
  • Print preview
• Import/export of data and graphics
  • Standard import
    • External files
  • Import tracks
    • GFF3 format
  • Import high-throughput sequencing data
    • Roche 454
    • Illumina
    • PacBio
    • SOLiD
    • Fasta read files
    • Sanger sequencing data
    • Ion Torrent
    • Complete Genomics
    • General notes on handling paired data
    • SAM and BAM mapping files
  • Import RNA spike-in controls
  • 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 tables
  • Export graphics to files
    • File formats
  • Export graph data points to a file
  • Copy/paste view output
• Data download
  • SRA search
    • SRA search options
    • SRA search output
    • Downloading reads and metadata from SRA
    • How reads are downloaded
  • Sequence web info
• Running tools, handling results and batching
  • Running tools
  • Handling results
  • Batch processing
    • Standard batch processing
    • Batch overview
    • Parameters for batch runs
    • Running the analysis and organizing the results
    • Batch launching workflows with multiple inputs
• Viewing and editing sequences
  • View sequence
    • Sequence settings in 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
• Viewing structures
  • Importing molecule structure files
  • Viewing molecular structures in 3D
  • Customizing the visualization
    • Visualization styles and colors
    • Project settings
  • 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
• Reference data for ready-to-use workflows
  • Download and configure reference data
  • Create a custom Reference Data Set
  • Exporting reference data for use in external applications
  • Troubleshooting reference data downloads
• Preparing raw data
  • Prepare Overlapping Raw Data (not recommended)
  • Prepare Raw Data (recommended)
    • Output from the Prepare Raw Data workflow
    • 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
• Genome browser
  • Create new genome browser view
  • Genome browser view tools
    • Adding ideogram to Genome Browser View
    • Zooming and navigating the genome browser view
    • 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
  • Graphs
    • Create GC Content Graph
    • Create Mapping Graph
    • Identify Graph Threshold Areas
• 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
    • QC Sequencing Report Content
    • Adapters
    • Running the 'QC for Sequencing Reads' tool
  • QC for Read Mapping
    • Running the 'QC for Read Mapping' tool
• Preparing raw data tools
  • Merge overlapping pairs
    • Using quality scores when merging
    • Report of merged pairs
  • Trim Sequences
    • Quality trimming
    • Adapter trimming
    • Creating a new Trim adapter list
    • Length trimming
    • Trim output
  • Demultiplex reads
    • An example using Illumina barcoded sequences
• Resequencing analysis tools
  • 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
    • Mapping output options
    • Mapped reads coloring
    • Reads track output from a read mapping
  • Summary mapping report
  • Mapping SOLid reads in color space
    • Viewing color space information
    • Mapping in color space
  • 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
  • Remove duplicate mapped reads
    • Algorithm details and parameters
    • Running the duplicate reads removal
  • Extract reads based on overlap
  • 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
  • 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
  • Coverage analysis
  • Variant Detectors - overview
    • Differences in the variants called by the different tools
    • How the variant detection tools work
  • Fixed Ploidy Variant Detection
    • Ploidy and sensitivity
  • Low Frequency Variant Detection
  • Basic 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
  • Variant data
    • Variant tracks
    • The annotated variant table
    • Variant types
  • Detailed information about overlapping paired reads
  • Identify Known Mutations from Sample Mappings
    • How to run the Identify Known Mutations from Sample Mappings tool
    • Output from the Identify Known Mutations from Sample Mappings workflow
• 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
• RNA-Seq Analysis tools
  • RNA-Seq analysis
    • Specifying reads and reference
    • Defining mapping options for RNA-Seq
    • The EM estimation algorithm
    • Calculating expression values from RNA-Seq
    • Specifying RNA-Seq outputs
    • Expression tracks
    • Reads track
    • RNA-Seq report
    • Gene fusion reporting
  • Create Combined RNA-Seq Report
  • Create fold change track
  • Advanced RNA-Seq Tools
    • TMM Normalization
    • Metadata for RNA-Seq
  • PCA for RNA-Seq
    • Principal component analysis plot (2D)
    • Principal component analysis plot (3D)
  • Differential Expression for RNA-Seq
    • The statistical model
    • Output of the Differential Expression for RNA-Seq tool
    • Statistical comparison tracks
    • The volcano plot
  • Create Heat Map for RNA-Seq
    • Clustering of features and samples
    • The heat map view
  • Create Expression Browser
    • The expression browser
  • Create Venn Diagram for RNA-Seq
    • Venn diagram table view
  • Gene Set Test
• Microarray and Small RNA Analysis tools
  • 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
    • 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
• Cutting and cloning
  • Restriction site analyses
    • Dynamic restriction sites
    • Restriction Site Analysis
  • Restriction enzyme lists
  • 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)
  • Gel electrophoresis
    • Gel view
• Sequencing Data Analysis
  • Importing and viewing trace data
    • Trace settings in the Side Panel
  • Trim sequences
    • Trimming using the Trim tool
    • Manual trimming
  • Assemble sequences
  • Assemble sequences to reference
  • Sort sequences by name
  • Add sequences to an existing contig
  • View and edit contigs and read mappings
    • View settings in the Side Panel
    • Editing a contig or 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
  • Standard PCR
    • When a single primer region is defined
    • When both forward and reverse regions are defined
    • Standard PCR output table
  • Nested PCR
  • TaqMan
  • Sequencing primers
  • 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
    • Output
    • Input
    • Layout
    • Input modifying tools
    • Workflow validation
    • Workflow creation helper tools
    • Adding to workflows
    • Snippets in workflows
    • Change the order of tracks in the Genome Browser View
  • Distributing and installing workflows
    • Creating a workflow installation file
    • Installing a workflow
    • Managing workflows
    • Workflow identification and versioning
    • Automatic update of workflow elements
  • Executing a workflow
  • Open copy of ready-to-use workflow
• 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

Install

To install a plugin, click the Download Plugins tab. This will display an overview of the plugins that are available for download and installation (see figure 1.24).

Figure 1.24: The plugins that are available for download.

Select the plugin of interest to display additional information about the plugin on the right side of the dialog. Click Download and Install to add the plugin functionalities to your workbench.

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Subsections

• Accepting the license agreement

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