bio-atac-seq-atac-peak-calling skillA
bio-atac-seq-atac-peak-calling is agent-read markdown (skill) from pku-yuangroup/openai4s: 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..
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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` …
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How to install
mdr add pku-yuangroup/openai4s/bio-atac-seq-atac-peak-calling@git:20260821.2d1b678mdr add pku-yuangroup/openai4s/bio-atac-seq-atac-peak-calling@sha256:a8d3b3bbfc9f185fPin to a label to follow the author's releases, or to a sha256 to freeze the exact bytes forever. Either way the resolved hash is written to mdr.lock, and mdr install reproduces it on any machine.
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Source
pku-yuangroup/openai4s · 586 stars · license MIT · pushed 2026-09-23 · branch main
API
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