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.