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• Welcome to CLC Cancer Research Workbench
  • Introduction to CLC Cancer Research Workbench
  • Available documentation
  • The material covered by this manual
  • We welcome your comments and suggestions
  • Contact information
• Introduction to user interface, workflows, and tracks
  • The start screen
    • The getting started table
    • Import of example data
  • The user interface
    • The Toolbox
  • Workflows - an overview
  • The track format
    • Track types
    • The Genome Browser
• 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
• How to edit application workflows
  • Introduction to customized data analysis
  • How to edit preinstalled workflows
• Using data from other workbenches
  • Open outputs from other workbenches
• Plugins
• Appendix
  • Workflows
  • Reference data overview
  • Mini dictionary
• Bibliography

The material covered by this manual

This usermanual provides introductory material on how to work with the software, including the import and initial handling of data and a guide to the data types and user interface. Its main focus is to provide guidance on how to use the workflows that come with the software.

Also included is an appendix where there is a table listing the available reference data as well as a small dictionary of terminology used in the CLC Cancer Research Workbench. The dictionary is not exhaustive, but we hope it will serve as a useful reference, especially for new users.

For comprehensive descriptions of the features and functionalities of the individual tools, please refer to the CLC Cancer Research Workbench reference manual.

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