The Assay for Transposase-Accessible Chromatin followed by sequencing (ATAC-seq) experiment provides genome-wide profiles of chromatin accessibility. Briefly, the ATAC-seq method works as follows: loaded Tn5 transposase inserts sequencing primers into open chromatin sites across the genome, and reads are then sequenced. The ends of the reads mark open chromatin sites.
The developed pipeline maps trimmed paired-end Illumina reads from mouse strains, to strain specific references. Mapped reads are then filtered to remove duplicates, mitochondrial reads, and reads that are not properly paired. Reads are shifted 4 bp to the right and reads on the negative strands should be shifted 5 bp to the left to accommodate Tn5 cut positioning. Peaks are then called with Macs2, and sequence coverage (depth) under peaks is then calculated.
Quality control metrics are also calculated. Trimmed read statistics, mapping statistics, percent mitochondrial DNA, percent duplication, insert size estimation, library complexity statistics, and fraction of reads in peak.