Documentation for CHi-C Pipeline

Table of Contents

• Requirements and Installation
  • Requirements
  • Installation
• Full Installation
  • Setup the System Environment
  • Setup pyenv and pyenv-virtualenv
  • Installation Process
  • Setup the symlinks
  • Prepare the Python Environment
• Pipelines
  • Map and parse CHi-C reads
  • Create CHiCAGO input RMAP
  • Create CHiCAGO input BAITMAP
  • Create CHiCAGO input Design files
  • Convert BAM file into chicago input files .chinput
  • Data normalization and peak calling
  • Run the entire CHi-C pipeline
• Tools for processing fastq C-HiC files
  • Map and parser reads
  • Create CHiCAGO input files
  • Convert bam files into chicago input
  • Normalize data and call C-HiC peaks
• Architectural Design Record
  • 25-09-2018 handling_chr_header branch merge with master
  • 15-10-2018 mm_mods_for_makebaitmaps branch merge with master
• License

Indices and tables

• Index
• Module Index
• Search Page