# Bio Atac Seq Atac Qc

Quality control metrics for ATAC-seq data including fragment size distribution, TSS...

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

## Description

Quality control metrics for ATAC-seq data including fragment size distribution, TSS enrichment, FRiP, and library complexity. Use when assessing ATAC-seq library quality before or after peak calling to identify problematic samples.

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

## Version Compatibility

Reference examples tested with: bedtools 2.31+, deepTools 3.5+, numpy 1.26+, pandas 2.2+, picard 3.1+, 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.

# ATAC-seq Quality Control

**"Check the quality of my ATAC-seq library"** → Evaluate fragment size distribution (nucleosome periodicity), TSS enrichment, FRiP, and library complexity to assess chromatin accessibility experiment quality.
- CLI: `deeptools bamPEFragmentSize`, `picard CollectInsertSizeMetrics`
- Python: `pysam` for custom fragment analysis

## Fragment Size Distribution

**Goal:** Assess ATAC-seq library quality by visualizing the characteristic nucleosome periodicity in fragment sizes.

**Approach:** Extract insert sizes from the BAM file using Picard or samtools, producing a distribution that should show NFR (<100 bp) and mono-nucleosome (~200 bp) peaks.

```bash
# Using Picard
java -jar picard.jar CollectInsertSizeMetrics \
    I=sample.bam \
    O=insert_sizes.txt \
    H=insert_sizes.pdf \
    M=0.5

# Using samtools
samtools view -f 66 sample.bam | \
    awk '{print sqrt($9^2)}' | \
    sort | uniq -c | \
    awk '{print $2"\t"$1}' > fragment_sizes.txt
```

## TSS Enrichment Score

**Goal:** Quantify signal enrichment at transcription start sites as a key ATAC-seq quality metric.

**Approach:** Create a TSS BED file, compute a signal matrix around TSS positions using deepTools, then plot the enrichment profile.

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