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• Introduction to Biomedical Genomics Workbench
  • Contact information
    • Contact for the Biomedical Genomics Workbench
    • New program feature request
    • Getting help
  • 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
    • Import of example data
  • Plugins
    • Installing plugins
    • Uninstalling plugins
    • Updating plugins
  • Network configuration
• User interface
  • View Area
    • Open view
    • Open additional views with the toolbar
    • 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
    • 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
    • Importing Metadata
    • Associating data elements with metadata
    • Working with data and metadata
  • Working with tables
    • Filtering tables
  • 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
• Data download
  • SRA search
    • SRA search options
    • SRA search output
    • Downloading reads and metadata from SRA
    • How reads are downloaded
  • Sequence web info
• User preferences and settings
  • General preferences
  • View preferences
    • 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
  • 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
    • GFF3 format
  • Import high-throughput sequencing data
    • Roche 454
    • Illumina
    • SOLiD
    • Fasta read files
    • Sanger sequencing data
    • Ion Torrent
    • 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 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
• 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
    • 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
    • Create a custom Reference Data Set
    • Exporting reference data for use in external applications
    • Troubleshooting reference data downloads
  • Create new folder
  • Import sequencing data
    • How to import data
  • Prepare sequencing data
    • 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
• 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
    • Length trimming
    • Trim output
  • Demultiplex reads
• 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
  • Trim primers of mapped reads
  • 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
    • Running the Coverage analysis tool
  • 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
• 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
    • The EM estimation algorithm
    • 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
  • 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
    • 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
    • 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
• Legacy tools
  • 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

Running tools, handling results and batching

This section describes how to run a tool using singles files as input, as well as how to handle and inspect results. We also review how to run tools using the batch mode when the option is enabled.

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Subsections

• Running tools
• Handling results
• Batch processing

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