Welcome to Diachromatic’s documentation

Contents:

• Program setup
  • Building Diachromatic from source
  • Preparation for bowtie2
• Tutorial with test data
  • Test dataset
  • Truncation
  • Mapping
  • Counting
  • Summarize
• In silico genome digest
  • Performing the in silico digest using GOPHER
  • Format of the digest file
• Truncation of chimeric Hi-C reads
  • Running the truncate subcommand
  • Output files
• Mapping paired-end Hi-C reads
  • Independent mapping of forward and reverse paired-end reads
  • Pairing of properly mapped read pairs
  • Running the align subcommand
  • Output files
• Counting unique valid pairs
  • Required input files
  • Running the count subcommand
  • Output files
• Summarize results
  • Running the summarize subcommand
  • Output files

Differential Analysis of Chromatin Interactions by Capture (Diachromatic)

Diachromatic is a Java application that implements a capture Hi-C preprocessing pipeline followed by analysis of differential chromatin interactions (“loopings”). Diachromatic is designed to work with the capture probes as designed by GOPHER.

Generator Of Probes for capture Hi-C Expriments at high Resolution (GOPHER)

GOPHER is a Java application designed to help design capture probes for capture Hi-C and related protocols. Capture Hi-C (CHC) is based on the Hi-C protocol but uses capture baits (similar to whole-exome sequencing) to enrich a set of viewpoints. Commonly, the viewpoints represent proximal promoter regions (surrounding the transcription start site [TSS]) of genes of interest or of all protein-coding genes. CHC detects interactions between viewpoint regions and distal enhancers (or other genomic regions) and has been most commonly performed with the 4-cutter DpnII or with the 6-cutter HindIII.