CHi-C

This repository contains pipelines for analyzing capture Hi-C data. CHiCAGO algorithm is used for the normalization of chromatin contacts

Requirements

• pyenv and pyenv-virtualenv

• Python 2.7.12

• Python Modules:

  • pylint
  • pytest
  • mg-tool-api
  • rpy2
  • matplotlib
  • pandas
  • rtree
  • scipy
  • numpy
  • rtree

• R >=3.1.2 -R Modules: -argparser -devtools -Chicago

• bedtools

• perl

• spatialindex

• bowtie2

• hicup

• BWA

Installation

For a guide to the full installation procedure the see ReadTheDocs

Directly from GitHub:

.. code-block:: none :linenos:

cd ${HOME}/code

git clone -b VM_CR1 https://github.com/Multiscale-Genomics/CHi-C.git

cd CHi-C

Create the Python environment

.. code-block:: none :linenos:

pyenv-virtualenv 2.7.10 CHi-C pip install --editable .

Tests

Tests must be runned from the top directory. Test for single tools are runned with pytest, example: $pytest tests/test_rmap_tool.py There is an order to run single tests:

• test_rmap_tool.py
• test_baitmap.py
• test_design.py
• test_hicup.py
• test_bam2chicago.py
• test_pyCHiC.py

To run all test type: $python tests/test_toolchains.py

IMPORTANT! From the top directory type ./tidy_data before running tests/test_toolchains.py