AtacFlow

Analysis pipeline for ATAC-seq data using Nextflow

This pipeline inspired by and based on the ENCODE ATAC-seq processubg pipeline and the prototype ATAC-seq pipeline developed by Anshul Kundaje's lab at Stanford University

Installation

• Install Nextflow
• Clone repository
  • using nextflow: nextflow clone DoaneAS/atacflow ./
  • or using git: git clone https://github.com/DoaneAS/atacflow.git
• Install conda dependencies:

  conda update conda
  conda env create --file requirements.atacFlow.yml
  conda env create --file deep.yml
  

Setup data

• ATAC-seq reads go in data/<Sample>/*_001.fastq.gz
  • Concatenate read pairs per sample parallel -j8 './bin/catlanes.sh {}' ::: data/Sample*
• Create sample index: python bin/makeIndex.py

Execution

nextflow run -with-trace -with-dag flow.html main.nf --index sampleIndex.csv --genome hg38

• supported genomes on panda WCM cluster: hg38, mm10