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CHi-C

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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