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 portable manner. It comes with Docker containers, making installation trivial and results highly reproducible.

nf-core/atacseq

https://github.com/nf-core/atacseq

ATAC-seq peak-calling and QC analysis pipeline - https://nf-co.re/atacseq

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When we run analysis

We run this analysis for projects where NGI generated the libraries and only upon request and on a case-by-case basis. The analysis has been set up for human, mouse, zebrafish, and Drosophila. 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

Results

• 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: 25th February 2026