CCanalyser documentation

CCanalyser is a package explicitly designed for processing Capture-C, Tri-C and Tiled-C data. It consists of a configurable data processing pipeline and a supporting command line interface to enable fine-grained control over the analysis. Unlike other pipelines that are designed to process Hi-C or Capture-HiC data, the filtering steps in ccanalyser are specifically optimised Capture-C, Tri-C and Tiled-C. This package is effectively a python based re-implementation of CCseqBasicS, Tri-C, Tiled-C and CaptureCompare designed to provide an end-to-end solution for processing data from these three assays.

• Installing
  • Pre-Installation recommendations
  • Installation
• Pipeline
  • Step 1 - Create a working directory
  • Step 2 - Edit a copy of config.yml
  • Step 3 - Copy or link fastq files into the working directory
  • Step 4 - Running the pipeline
  • Step 5 - Running the pipeline to a specified stage
  • Pipeline outputs
• Pipeline FAQ
  • Interruptions to the pipeline
  • DRMAA error
  • KeyError: ‘missing parameter accessed’
  • ValueError: not enough values to unpack (expected 2, got 1)
• CLI Documentation
  • ccanalyser
• Module Documentation
  • CCanalyser Modules
• Glossary