Browse the manual

• Introduction to CLC Cancer Research 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 and management
  • 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
  • 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
    • 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
    • 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
  • 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
• 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 data
    • How to import data
• Preparing Raw Data
  • Prepare sequencing data - all application types
    • 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
  • Analysis of sequencing data
• Whole genome sequencing (WGS)
  • Automatic analysis of sequencing data (WGS)
  • Identify Variants (WGS)
    • How to run the 'Identify Variants' ready-to-use workflow
    • Output from the Identify Variants workflow
  • Annotate Variants (WGS)
  • Filter Somatic Variants (WGS)
  • Identify Somatic Variants from Tumor Normal Pair (WGS)
  • Identify Known Variants in One Sample (WGS)
    • Import your known variants
    • Import your targeted regions
    • How to run the 'Identify Known Variants in One Sample' ready-to-use workflow
    • Output from the Identify Known Variants in One Sample
• Whole exome sequencing (WES)
  • Automatic analysis of sequencing data (WES)
  • Identify Variants (WES)
    • Import your targeted regions
    • How to run the 'Identify Variants' ready-to-use workflow
    • Output from the Identify Variants workflow
  • Annotate Variants (WES)
  • Filter Somatic Variants (WES)
  • Identify Somatic Variants from Tumor Normal Pair (WES)
    • Import your targeted regions
    • How to run the 'Identify Somatic Variants from Tumor Normal Pair' ready-to-use workflow
  • Identify Known Variants in One Sample (WES)
    • Import your known variants
    • Import your targeted regions
    • How to run the 'Identify Known Variants in One Sample' ready-to-use workflow
    • Output from the Identify Known Variants in One Sample
  • Identify and Annotate Variants (WES)
    • Import your targeted regions
    • How to run the 'Identify and Annotate Variants' ready-to-use workflow
    • Output from the Identify and Annotate Variants workflow
• Targeted amplicon sequencing (TAS)
  • Automatic analysis of sequencing data (TAS)
  • Identify Variants (TAS)
    • Import your targeted regions
    • How to run the 'Identify Variants' ready-to-use workflow
    • Output from the Identify Variants workflow
  • Annotate Variants (TAS)
  • Filter Somatic Variants (TAS)
  • Identify Somatic Variants from Tumor Normal Pair (TAS)
    • Import your targeted regions
    • How to run the 'Identify Somatic Variants from Tumor Normal Pair' ready-to-use workflow
  • Identify Known Variants in One Sample (TAS)
    • Import your known variants
    • Import your targeted regions
    • How to run the 'Identify Known Variants in One Sample' ready-to-use workflow
    • Output from the Identify Known Variants in One Sample
  • Identify and Annotate Variants (TAS)
    • Import your targeted regions
    • How to run the 'Identify and Annotate Variants' ready-to-use workflow
    • Output from the Identify and Annotate Variants workflow
• Whole Transcriptome Sequencing (WTS)
  • Automatic analysis of RNA-seq data
  • 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 contents
    • 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
    • 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
  • Remove duplicate mapped reads
    • Algorithm details and parameters
    • Running the duplicate reads removal
  • Coverage analysis
    • Running the Coverage analysis tool
  • Variant Detectors - overview
    • Differences among the variants called by the three variant callers
    • How the variant detectors 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
    • How the protein structures are found
    • Create 3D visualization of variant
    • 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
  • Create Filter Criteria
  • 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
    • Visualizing RNA-Seq read tracks for the experiment
    • 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
  • 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
• 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 ChIP-Seq Analysis 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
  • 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

List of shortcuts

The keyboard shortcuts in CLC Cancer Research Workbench are listed below.

Action	Windows/Linux	Mac OS X
Adjust selection	Shift + arrow keys	Shift + arrow keys
Adjust workflow layout	Shift + Alt + L	+ Shift + Alt + L
Close	Ctrl + W	+ W
Close all views	Ctrl + Shift + W	+ Shift + W
Copy	Ctrl + C	+ C
Create track list	Ctrl + L	+ L
Cut	Ctrl + X	+ X
Delete	Delete	Delete or + Backspace
Exit	Alt + F4	+ Q
Export	Ctrl + E	+ E
Export graphics	Ctrl + G	+ G
Find Next Conflict	'.' (dot)	'.' (dot)
Find Previous Conflict	',' (comma)	',' (comma)
Help	F1	F1
Import	Ctrl + I	+ I
Maximize/restore size of View	Ctrl + M	+ M
Move gaps in alignment	Ctrl + arrow keys	+ arrow keys
New Folder	Ctrl + Shift + N	+ Shift + N
Panning Mode	Ctrl + 4	+ 4
Paste	Ctrl + V	+ V
Print	Ctrl + P	+ P
Redo	Ctrl + Y	+ Y
Rename	F2	F2
Save	Ctrl + S	+ S
Save As	Ctrl + Shift + S	+ Shift + S
Scrolling horizontally	Shift + Scroll wheel	Shift + Scroll wheel
Search local data	Ctrl + Shift + F	+ Shift + F
Search via Side Panel	Ctrl + F	+ F
Select All	Ctrl + A	+ A
Select Selection Mode	Ctrl + 1 (one)	+ 1 (one)
Show folder content	Ctrl + O	+ O
Show/hide Side Panel	Ctrl + U	+ U
Sort folder	Ctrl + Shift + R	+ Shift + R
Split Horizontally	Ctrl + T	+ T
Split Vertically	Ctrl + J	+ J
Start Tool Quick Launch	Ctrl + Shift + T	+ Shift + T
Undo	Ctrl + Z	+ Z
Update folder	F5	F5
User Preferences	Ctrl + K	+ ;
Vertical scroll in read tracks	Alt + Scroll wheel	Alt + Scroll wheel
Vertical scroll in reads tracks, fast	Shift+Alt+Scroll wheel	Shift+Alt+Scroll wheel
Vertical zoom in graph tracks	Alt + Scroll wheel	Alt + Scroll wheel

Action	Windows/Linux	Mac OS X
Reverse zoom mode	press and hold Shift	press and hold Shift
Workflow, add element	Alt + Shift + E	Alt + Shift + E
Workflow, collapse if its expanded	Alt + Shift + '-' (minus)	Alt + Shift + '-'
Workflow, create installer	Alt + Shift + I	Alt + Shift + I
Workflow, execute	Ctrl + enter	+ enter
Workflow, expand if its collapsed	Alt + Shift + '+' (plus)	Alt + Shift + '-'
Workflow, highlight used elements	Alt + Shift + U	Alt + Shift + U
Workflow, remove all elements	Alt + Shift + R	Alt + Shift + R
Zoom	Ctrl + Scroll wheel	Ctrl + Scroll wheel
Zoom In Mode	Ctrl + 2	+ 2
Zoom In (without clicking)	'+' (plus)	'+' (plus)
Zoom Out Mode	Ctrl + 3	+ 3
Zoom Out (without clicking)	'-' (minus)	'-' (minus)
Zoom to base level	Ctrl + 0	+ 0
Zoom to fit screen	Ctrl + 6	+ 6
Zoom to selection	Ctrl + 5	+ 5

Combinations of keys and mouse movements are listed below.

Action	Windows/Linux	Mac OS X	Mouse movement
Maximize View			Double-click the tab of the View
Restore View			Double-click the View title
Reverse zoom mode	Shift	Shift	Click in view
Select multiple elements that are not grouped together	Ctrl		Click elements
Select multiple elements that are grouped together	Shift	Shift	Click elements

"Elements" in this context refers to elements and folders in the Navigation Area selections on sequences, and rows in tables.

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