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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

Introduction to Biomedical Genomics Workbench

Welcome to Biomedical Genomics Workbench 3.5 -- a software package supporting your daily bioinformatics work.

This user manual can also be found in pdf format: User_Manual.pdf

This software is for research purposes only.

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Subsections

• Contact information
• Download and installation
• System requirements
• Workbench Licenses
• When the program is installed: Getting started
• Plugins
• Network configuration

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