Route: atac

ATAC-seq analysis.


  • Align to the reference genome (Bowtie2).
  • Remove duplicate reads (Sambamba).
  • Generate genome browser tracks.
  • Call peaks (MACS and HMMRATAC).


Set up a new analysis (common across all routes). If running for the first time, check the detailed usage instructions for an explanation of every step.

cd <project dir>
git clone --depth 1
sns/generate-settings <genome>
sns/gather-fastqs <fastq dir>

Run atac route.

sns/run atac

Check for potential problems.

grep "ERROR:" logs-sbatch/*


Primary results:

  • BAM-DD: Deduplicated BAM files. Can be used for additional analysis.
  • BIGWIG: BigWig files normalized to the total number of reads. Can be used for visual inspection of peaks.
  • peaks-*: Peaks.

Run metrics:

  • summary-combined.atac.csv: Summary table that includes the number of reads, alignment rate, and fraction of PCR duplicates.
  • summary.qc-fragment-sizes.png: Distribution of fragment sizes.