# Atacseq Qc

> ATAC-seq Quality Control

- Skill: `diegosouzapw/atacseq-qc-2` (Agent Skill, multi-file: 2 files)
- Install (CLI): `npx skillmds@latest add diegosouzapw/atacseq-qc-2`
- Raw SKILL.md: https://api.skillmd.com/api/skills/diegosouzapw/atacseq-qc-2/raw
- Safety review: pending (external: skill-scanner PASS, skillspector PASS)
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Coding & Dev Tools
- Author: diegosouzapw (https://skillmd.com/u/diegosouzapw)
- Updated: 2026-09-21
- Page: https://skillmd.com/skills/diegosouzapw/atacseq-qc-2

---


# ATAC-seq Quality Control

## Overview

This skill performs complete ATAC-seq data quality control from BAM and peak files.

Main steps include:
- Refer to the **Inputs & Outputs** section to check inputs and build the output architecture. All the output file should located in `${proj_dir}` in Step 0.
- **Always prompt user** for genome assembly used. Never decide by yourself. 
- Generate TSS files according to genome assembly.
- Compute TSS enrichment, fragment distribution and FRiP. 

---

## Inputs & Outputs

### Inputs

```bash
${sample}.bam # filtered bam files
${sample}.narrowPeak
```

### Outputs

```bash
all_atac_qc/
    ${sample}_qc_results/
        ataqv_metrics.json
        ataqv_report.html/
    temp/
```

---

## Decision Tree

### Step 0: Initialize Project

Call:

- `mcp__project-init-tools__project_init`

with:

- `sample`: all
- `task`: atac_qc
- `genome`: provided by user

The tool will:

- Create`all_atac_qc` directory.
- Return the full path of the `all_atac_qc` directory, which will be used as `${proj_dir}`.

### Step 1: Detect the name logic of the chromosomes in BAM file (have "chr" as prefix or not)

`samtools view <sample>.bam | head -n 10 | cut -f 3`

### Step 2: Generate reference files

Call:
- mcp__qc-tools__generate_reference

with:
- `genome`: Genome name (e.g., hg38), provided by user
- `temp_dir`: ${proj_dir}/temp
- `bam_uses_chr`: True if BAM uses 'chr' prefix (chr1), False if not (1).

### Step 3: Peform quality control for the ATAC-seq data

Call:
- mcp__qc-tools__run_ataqv_qc

- `bam_file`: Path to filtered BAM file
- `peak_file`: Path to peak file (narrowPeak) corresponding to the BAM file
- `tss_file`: ${proj_dir}/temp/${genome}.tss
- `species`: Species used, choose from (fly, human, mouse, rat, worm, yeast)
- `bam_uses_chr`: True if BAM uses 'chr' prefix (chr1), False if not (1).
- `output_dir`: ${proj_dir}/${sample}_qc_results
- `autosomal_ref_path`: Provided if `bam_uses_chr` is False, ${proj_dir}/temp/${genome}.autosomal.ref