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

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

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

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