ATAC-seq analysis

Bioinformatic analysis pipeline for ATAC-seq data

nfcore/atacseq is a bioinformatics analysis pipeline used for ATAC-seq data.

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible.

When we run analysis

We run this analysis for projects were NGI generated the data and only on request and on a case-by-case basis.

If you have prepared a library yourself and we are just sequencing, please get in touch and mention that you would like us to run this analysis.

The analysis works with any of the species that have a reference genome available in AWS-iGenomes. If in doubt, please ask whether we can run the pipeline for you.

Input data

  • FastQ files
  • sample sheet (with sample names, path to fastQ files, information about replicates)
  • reference genome information


  • Raw read QC based on FastQC
  • Statistics about
    • adapter trimming efficiency
    • mapping efficiency
    • deduplication
    • insert size
    • estimated library complexity
    • coverage
    • read distribution around transcriptional start sites
    • peak distribution
  • Normalized BigWig files
  • Peaks called by MACS2 and annotated by Homer
    • peak consensus file (BEDtools)
  • Read counts and differential binding (DESeq2)
  • Pipeline info

Last Updated: 15th May 2024

Please read our sample submission instructions before sending samples:

Sample Submission Guidelines
Method Status


We are currently testing this method. Please contact us to find out more.

Software tool versions

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Compatible Methods