• Manuals

Browse the manual

• 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

Graphical QC Report

• 1 Summary
• 2 Per-sequence analysis
• 2.1 Lengths distribution
• 2.2 GC-content
• 2.3 Ambiguous base-content
• 2.4 Quality distribution
• 3 Per-base analysis
• 3.1 Coverage
• 3.2 Nucleotide distributions
• 3.3 GC-content
• 3.4 Ambiguous base-content
• 3.5 Quality distribution
• 4 Over-representation analyses
• 4.1 Enriched 5mers
• 4.2 Sequence duplication levels
• 4.3 Duplicated sequences

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