README.md

SRAtac

A pipeline for ATAC-seq data analysis built on SRAlign.

Introduction

SRAtac is a Nextflow pipeline for processing ATAC-seq data.

SRAtac is designed to be highly flexible pipeline for ATAC-seq data processing. The goal of this pipeline is to perform end-to-end data processing of ATAC-seq samples with extensive QC at all steps.

Pipeline overview

1. Trim reads
2. QC of reads
   1. Raw reads FastQC
   2. Trim reads FastQC
   3. Summary MultiQC
3. Align reads
   1. Align to reference genome/transcriptome
   2. Check contamination
4. Preprocess alignments
   1. Mark duplicates
   2. Compress sam to bam
   3. Index bam
5. QC of alignments
   1. samtools stats
   2. Samtools index stats
   3. Percent duplicates
   4. Percent aligned to contamination reference
   5. Summary MultiQC
6. Library complexity and reproducibility
   1. Preseq library complexity
   2. DeepTools correlation
   3. DeepTools PCA
7. Full pipeline MultiQC

Quick start

1. Install Nextflow
2. Install Docker
3. Download SRAtac:

   nextflow pull trev-f/SRAtac
   

4. Run SRAtac in test mode:

   nextflow run trev-f/SRAtac -profile test 
   

5. Run your analysis:

   nextflow run trev-f/SRAtac -profile docker --input <input.csv> --genome <valid genome key>
   

Detailed documentation can be found in docs and usage