# Bio Atac Seq Nucleosome Positioning

Extract nucleosome positions from ATAC-seq data using NucleoATAC, ATACseqQC, and...

- Repository: https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills (3090 stars)
- Category: Engineering
- License: see repository
- Last updated: 2026-07-21
- Runs scripts: no, instructions only

## Install

Claude Code: `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-atac-seq-nucleosome-positioning -g -a claude-code -y`
Codex: `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-atac-seq-nucleosome-positioning -g -a codex -y`
Cursor: `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-atac-seq-nucleosome-positioning -g -a cursor -y`
Gemini CLI: `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-atac-seq-nucleosome-positioning -g -a gemini-cli -y`

## Description

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.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

## Version Compatibility

Reference examples tested with: Rsamtools 2.18+, matplotlib 3.8+, numpy 1.26+, pyBigWig 0.3+, pysam 0.22+, samtools 1.19+

Before using code patterns, verify installed versions match. If versions differ:
- Python: `pip show <package>` then `help(module.function)` to check signatures
- R: `packageVersion('<pkg>')` then `?function_name` to verify parameters
- 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.

# Nucleosome Positioning

**"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.

## Background

ATAC-seq fragments reflect chromatin structure:
- **< 100 bp**: Nucleosome-free regions (NFR)
- **180-247 bp**: Mono-nucleosome
- **315-473 bp**: Di-nucleosome
- **558-615 bp**: Tri-nucleosome

## ATACseqQC (R)

### Installation

```r
BiocManager::install('ATACseqQC')
```

### Fragment Size Distribution

```r
library(ATACseqQC)
library(Rsamtools)

# Read BAM
bamfile <- 'sample.bam'

# Fragment size distribution
fragSize <- fragSizeDist(bamfile, 'sample')

# Nucleosome-free and mono-nucleosome ratios
# Automatic QC metrics
```

### Nucleosome Positioning

**Goal:** Map nucleosome positions around TSS using ATAC-seq fragment size classes.

**Approach:** Read BAM, apply Tn5 shift correction, split fragments into NFR and mono-nucleosome classes by size, then compute signal profiles around TSS.

```r
library(ATACseqQC)
library(TxDb.Hsapiens.UCSC.hg38.knownGene)
library(BSgenome.Hsapiens.UCSC.hg38)

The rest: https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/blob/HEAD/skills/bio-atac-seq-nucleosome-positioning/SKILL.md