ASAP - ATAC-Seq Analysis Pipeline

ASAP is a flexible analysis pipeline for ATAC-seq data analysis. Starting from raw ATAC-seq sequencing reads, ASAP outputs raw and filtered mapping files, coverage files (reads coverage ; tn5 insertion events coverage), fragment length distribution, read extraction based on fragment length, nucleosomes visualization and peak calling results.

Overview of main steps

• Mapping
• Post-mapping processing and filtering:
  • Filter (or not) reads that fall into user-defined blacklisted regions
  • Select reads that do not carry more than minMismatch and filter by minimum mapping quality (MAPQ)
  • Mark duplicated pairs
  • Select concordant, non-duplicated pairs.
  • Shift reads by 4bp as described in Schep et al.,2015: shift by 4bp toward to center of the transposition event.
• Compute read coverage
• Compute insertion events coverage
• Fragment length distribution
• Extract reads pairs based on a fragment length range and compute arcs between fragment extremities (protection visualization)
• Peak calling