Manuals
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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
Workflows
