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:20260719.44d7640Pins git:20260719.44d7640 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- fridrichmethod/awesome-skills
- Path
skills/atac-peak-calling/SKILL.md- Versions recorded
- 2
- Latest version
- git:20260719.44d7640, committed Jul 19, 2026
- First version recorded
- May 17, 2026
- Size
- 21,467 bytes
- Repository stars
- 15
- License
- a license file GitHub does not identify
Call accessible chromatin regions from ATAC-seq BAM files using MACS3, MACS2, Genrich, or HMMRATAC. Use when identifying open chromatin from aligned ATAC-seq, choosing between point-source vs HMM peak callers, applying ENCODE-style pseudoreplicate IDR, removing blacklist regions, or fixing 501bp consensus peaks for downstream differential analysis.
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: MACS3 3.0.2+, MACS2 2.2.9+, Genrich 0.6.1+, HMMRATAC 1.2+ (now bundled in MACS3 as `macs3 hmmratac`), samtools 1.19+, bedtools 2.31+, IDR 2.0.4+. Before using code patterns, verify installed versions match. If versions differ: - CLI: `<tool> --version` then `<tool> --help` to confirm flags If code throws unexpected errors, introspect the installed binary (`<tool> -h`) and adapt the example to match the actual CLI rather than retrying. # ATAC-seq Peak Calling **"Call accessible regions from my ATAC-seq BAM"** -> Identify Tn5-hypersensitive open chromatin, treating fragments as point insertion events (not protein-bound regions as in ChIP-seq) and accounting for the lack of input control. - CLI (canonical, ENCODE 4): `macs2 callpeak -t atac.bam -f BAM -g hs -n sample --nomodel --shift -75 --extsize 150 --keep-dup all -B --SPMR -p 0.01` (use `-f BAM`, not `-f BAMPE` -- BAMPE reads true fragment ends and ignores `--shift`/`--extsize`) - CLI (HMM-based, single sample): `macs3 hmmratac -i atac.bam -n sample --outdir hmm_out` …
Read the whole file at its exact version.
How to install
mdr add fridrichmethod/awesome-skills/bio-atac-seq-atac-peak-calling@sha256:aaf79f23f81d2d9aThe line at the top of this page pins the label git:20260719.44d7640, 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_7hyimscrelmecyiw)
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Versions
The registry has recorded 2 versions of this file, between May 17, 2026 and Jul 19, 2026, about one every 63 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260719.44d7640 latest | 2026-07-19 | 44d7640 | 21,467 B | A | view · diff |
| git:20260517.81511a7 | 2026-05-17 | 81511a7 | 20,653 B | A | view |
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (21467 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
fridrichmethod/awesome-skills · 15 stars · license a license file GitHub does not identify · pushed 2026-10-18 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_7hyimscrelmecyiw GET https://markdownregistry.com/api/v1/resolve?ref=fridrichmethod/awesome-skills/bio-atac-seq-atac-peak-calling GET https://markdownregistry.com/api/v1/blob/aaf79f23f81d2d9a15437a08d53a5305717eaf60e480396606e431133171eaa8
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.
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