README.md

ATAC-Seq

This repository contains pipeline wrapper for the analysis of ATAC Seq data. ATAC Seq protocols are used for transposase accessible chromatin regions.

Requirements

• pyenv and pyenv-virtualenv
• Python 2.7.12
• Python Modules:
  • pylint
  • pytest
  • mg-tool-api
• Cutadapt
• Bowtie2
• Trim Galore
• R

Installation

Directly from GitHub:

cd ${HOME}/code

git clone https://github.com/Multiscale-Genomics/mg-process-test.git

cd mg-process-test

Create the Python environment

pyenv-virtualenv 2.7.12 mg-process-test
pyenv activate mg-process-test
pip install -e .
pip install -r requirements.txt