MACS3 Peak Calling Starter

Use this skill to run a deterministic toy peak-calling example with MACS3 callpeak.

What it does

• Runs macs3 callpeak on a small BED file using --nomodel --extsize 75 so toy data can be verified reliably.
• Writes the standard narrowPeak, summits.bed, and peaks.xls outputs to a work directory.
• Summarizes the strongest peak into a compact JSON payload for tests and demos.

When to use it

• You need a runnable starter for simple ChIP-seq or chromatin-style peak calling.
• You want a deterministic local example before moving to real replicate-aware workflows.
• You need a smoke-testable wrapper around MACS3.

Example

slurm/envs/genomics/bin/python skills/epigenomics-and-chromatin/macs3-peak-calling-starter/scripts/run_macs3_peak_calling.py \
  --treatment skills/epigenomics-and-chromatin/macs3-peak-calling-starter/examples/toy_treatment.bed \
  --summary-out scratch/epigenomics/macs3_peak_summary.json

Verification

• Skill-local tests: python3 -m unittest discover -s skills/epigenomics-and-chromatin/macs3-peak-calling-starter/tests -p 'test_*.py'
• Expected summary: peak_count == 1 and top_peak["name"] == "toy_peak_1"