bio-atac-seq-atac-peak-calling

name	bio-atac-seq-atac-peak-calling
description	Call accessible chromatin regions from ATAC-seq data using MACS3 with ATAC-specific parameters. Use when identifying open chromatin regions from aligned ATAC-seq BAM files, different from ChIP-seq peak calling.
tool_type	cli
primary_tool	macs3

ATAC-seq Peak Calling

Basic MACS3 for ATAC-seq

# Standard ATAC-seq peak calling
macs3 callpeak \
    -t sample.bam \
    -f BAMPE \
    -g hs \
    -n sample \
    --outdir peaks/ \
    -q 0.05 \
    --nomodel \
    --shift -75 \
    --extsize 150 \
    --keep-dup all \
    -B

Key ATAC-seq Parameters

# Explained parameters
macs3 callpeak \
    -t sample.bam \        # Treatment BAM
    -f BAMPE \             # Paired-end BAM (uses fragment size)
    -g hs \                # Genome size: hs (human), mm (mouse)
    -n sample \            # Output name prefix
    --nomodel \            # Don't build shifting model
    --shift -75 \          # Shift reads to center on Tn5 cut site
    --extsize 150 \        # Extend reads to this size
    --keep-dup all \       
    -B \                   
    --call-summits