bio-atac-seq-atac-peak-calling SKILL.md skillA
bio-atac-seq-atac-peak-calling from fridrichmethod/awesome-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add fridrichmethod/awesome-skills/bio-atac-seq-atac-peak-calling@git:20260517.81511a7Pins git:20260517.81511a7 in mdr.lock. Pin the fingerprint instead.
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- SKILL.md skill
- Repository
- fridrichmethod/awesome-skills
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skills/bio-atac-seq-atac-peak-calling/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260517.81511a7, committed May 17, 2026
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- a license file GitHub does not identify
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.
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
## 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.
```bash
# Standard ATAC-seq peak calling
macs3 callpeak \
-t sample.bam \
-f BAMPE \
-g hs \
-n sample \
--outdir peaks/ \
-q 0.05 \
--nomodel \
--shift -75 \
…Read the whole file at its exact version.
How to install
mdr add fridrichmethod/awesome-skills/bio-atac-seq-atac-peak-calling@sha256:523ddc4d69cdb04aThe line at the top of this page pins the label git:20260517.81511a7, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_5hgeclowp6zzr3mi)
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Versions
The registry has recorded 1 version of this file, committed on May 17, 2026.
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Source
fridrichmethod/awesome-skills · 15 stars · license a license file GitHub does not identify · pushed 2026-11-02 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_5hgeclowp6zzr3mi GET https://markdownregistry.com/api/v1/resolve?ref=fridrichmethod/awesome-skills/bio-atac-seq-atac-peak-calling GET https://markdownregistry.com/api/v1/blob/523ddc4d69cdb04af77248a023f18d8dc58677e99d7602e2c1f6fe77c5f12ec2
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