macs3-peak-calling
Poisson-model peak caller for ChIP-seq/ATAC-seq BAMs. MACS3 callpeak finds enriched regions (TF sites or histone marks) vs input/IgG; outputs BED narrowPeak/broadPeak for motif analysis, annotation, and differential binding. Use narrow peaks for TF ChIP-seq and ATAC-seq; broad for H3K27me3, H3K9me3, and other broad marks.
npx skills add BioTender-max/awesome-bio-agent-skills --skill macs3-peak-calling --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# MACS3 — ChIP-seq and ATAC-seq Peak Caller ## Overview MACS3 (Model-based Analysis of ChIP-seq) identifies regions of significant read enrichment (peaks) from ChIP-seq, ATAC-seq, CUT&RUN, and CUT&TAG experiments. It models the fragment length distribution from paired-end data or estimates it from mono-nucleosomal read shifting in single-end data, then applies a Poisson model to identify fold-enrichment over an input/IgG control. MACS3 produces BED-format narrowPeak (for transcription factors) or broadPeak (for histone marks) files with signal and q-value tracks for visualization in IGV or UCSC Genome Browser. ## When to Use - Calling transcription factor binding peaks from ChIP-seq experiments (use `--nomodel --extsize 200` or let MACS3 estimate fragment length) - Identifying open chromatin regions from ATAC-seq experiments (use `--nomodel --shift -100 --extsize 200 -f BAMPE`) - Calling broad histone modification peaks (H3K27me3, H3K9me3, H3K36me3) with `--broad` - Generating peak signal tracks (bedGraph/bigWig) for genome browser visualization with `-B --SPMR` - Performing differential binding analysis: MACS3 peaks as input to DiffBind or DESeq2 - Use **HMMRATAC** (part of MACS3)
- Overview
- When to Use
- Prerequisites
- Quick Start
- Workflow
- Step 1: Prepare Input BAM Files
- Step 2: Call Narrow Peaks (TF ChIP-seq)
- Step 3: Call Broad Peaks (Histone Marks)
- Step 4: Call ATAC-seq Peaks
- Step 5: Generate Signal Tracks for Visualization
- Step 6: Annotate and Analyze Peaks
- Key Parameters
- Common Recipes
- Recipe 1: Batch Peak Calling for Multiple Samples
Install with pip or conda pip install macs3 or conda install -c bioconda macs3 Verify macs3 --version macs3 3.0.2 Call peaks for TF ChIP-seq (narrow peaks, with input control) macs3 callpeak \ wc -l peaks/sample_tf_peaks.narrowPeak
What does the macs3-peak-calling skill do?
Poisson-model peak caller for ChIP-seq/ATAC-seq BAMs. MACS3 callpeak finds enriched regions (TF sites or histone marks) vs input/IgG; outputs BED narrowPeak/broadPeak for motif analysis, annotation, and differential binding. Use narrow peaks for TF ChIP-seq and ATAC-seq; broad for H3K27me3, H3K9me3, and other broad marks.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill macs3-peak-calling --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.