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

Version Compatibility

Reference examples tested with: Bowtie2 2.5.3+, MACS3 3.0+, samtools 1.19+

Before using code patterns, verify installed versions match. If versions differ:

• CLI: <tool> --version then <tool> --help to confirm flags

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

ATAC-seq Peak Calling

"Call peaks from my ATAC-seq data" → Identify open chromatin regions using ATAC-specific parameters (no input control, shifted Tn5 cut sites, paired-end mode).

• CLI: macs3 callpeak -t atac.bam -f BAMPE -g hs --nomodel --shift -75 --extsize 150

Basic MACS3 for ATAC-seq

Goal: Identify open chromatin regions from ATAC-seq data using ATAC-specific peak calling parameters.

Approach: Run MACS3 in paired-end mode with Tn5 shift correction, no model building, and duplicate retention since ATAC-seq generates natural duplicates at accessible sites.