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Introduction to CLC Cancer Research Workbench
- Contact information
- System requirements
  - Limitations on maximum number of cores
- Licenses
- About CLC Workbenches
  - New program feature request
  - Getting help
- When the program is installed: Getting started
  - Import of example data
- Plugins
- Network configuration
User interface
- View Area
- Zoom and selection in View Area
- Toolbox and Status Bar
- Workspace
- List of shortcuts
Data organization and management
- Navigation Area
- Customized attributes on data locations
- Filling in values
- Sequence web info
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 tracks
- Import high-throughput sequencing data
- Import Primer Pairs
- Data export
- Export graphics to files
- 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
- How to handle results of analyses
  - Table outputs
  - Batch log
- Working with tables
  - Filtering tables
Viewing and editing sequences
- View sequence
- Circular DNA
  - Using split views to see details of the circular molecule
  - Mark molecule as circular and specify starting point
- Working with annotations
- Element information
- View as text
- Sequence Lists
Getting started
- Reference data
- Create new folder
- Import data
  - How to import data
Preparing Raw Data
- Prepare sequencing data - all application types
- 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)
Whole exome sequencing (WES)
- Automatic analysis of sequencing data (WES)
- Identify Variants (WES)
- 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)
- Identify and Annotate Variants (WES)
Targeted amplicon sequencing (TAS)
- Automatic analysis of sequencing data (TAS)
- Identify Variants (TAS)
- 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)
- Identify and Annotate Variants (TAS)
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
- Creating graph tracks
Quality control tools
- QC for Target Sequencing
- QC for Sequencing Reads
- 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
- Demultiplex reads
Resequencing analysis tools
- Identify Known Mutations from Sample Mappings
- Trim primers of mapped reads
- Map Reads to Reference
- Mapping output options
- Color space
- Mapping result
  - View settings in the Side Panel
- Local realignment
- 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
- InDels and Structural Variants
- Variant data
- 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 overlapping genes
- Add information from genomic regions
- From databases
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
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
- Small RNA analysis
- Experimental design
- Working with tracks and experiments
- Transformation and normalization
- Quality control
- Statistical analysis - identifying differential expression
  - Empirical analysis of DGE
  - 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
Helper tools
- Extract sequences
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
- 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
  - 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
- Analyze primer properties
- Find binding sites and create fragments
  - Binding parameters
  - Results - binding sites and fragments
- Order primers
Workflows
- Creating a workflow
- Distributing and installing workflows
- Executing a workflow
Legacy tools
- Quality-based variant detection
- Probabilistic variant detection
Appendix
- Use of multi-core computers
- Reference data overview
- 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
- Translation Tables
- Matrices for alignment calculation
Bibliography

Viewing annotations

Annotations can be viewed in a number of different ways:

As arrows or boxes in all views displaying sequences (sequence lists, alignments etc)
In the table of annotations ().
In the text view of sequences ()

In the following sections, these view options will be described in more detail. In all the views except the text view (

), annotations can be added, modified and deleted. This is described in the following sections.

Subsections