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bio-atac-seq-nucleosome-positioning

Maintainer FreedomIntelligence · Last updated April 1, 2026

Extract nucleosome positions from ATAC-seq data using NucleoATAC, ATACseqQC, and fragment analysis. Use when analyzing chromatin organization, identifying nucleosome-free regions at promoters, or characterizing nucleosome occupancy patterns from ATAC-seq fragment size distributions.

OpenClawNanoClawAnalysisReproductionbio-atac-seq-nucleosome-positioning🧬 bioinformatics (gptomics bio-* suite)bioinformatics — epigenomics & chromatinextract

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-atac-seq-nucleosome-positioning

Maintainer: FreedomIntelligence
License: MIT
Last updated: April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

CLI: nucleoatac run --bed peaks.bed --bam atac.bam --fasta ref.fa.
R: ATACseqQC::splitGAlignmentsByCut() for fragment separation.
Map nucleosome positions from ATAC-seq" → Separate nucleosome-free and mono-nucleosome fragments by size, then call nucleosome center positions and occupancy scores. CLI: nucleoatac run --bed peaks.bed --bam atac.bam --fasta ref.fa R: ATACseqQC::splitGAlignmentsByCut() for fragment separation.
Extract nucleosome positions and occupancy from ATAC-seq fragment size patterns.
< 100 bp: Nucleosome-free regions (NFR).

Source Doc

Excerpt From SKILL.md

Fragment Size Distribution

library(ATACseqQC)
library(Rsamtools)

## Fragment size distribution

fragSize <- fragSizeDist(bamfile, 'sample')

## Get TSS regions

txs <- transcripts(TxDb.Hsapiens.UCSC.hg38.knownGene)
tss <- promoters(txs, upstream=1000, downstream=1000)

Use cases

Use when analyzing chromatin organization, identifying nucleosome-free regions at promoters, or characterizing nucleosome occupancy patterns from ATAC-seq fragment size distributions.