ATACseq-QC
Performs ATAC-specific biological validation. It calculates metrics unique to chromatin accessibility assays, such as TSS enrichment scores and fragment size distributions (nucleosome banding patterns). Use this skill when you have filtered BAM file and have called peak for the file. Do NOT use this skill for ChIP-seq data or general alignment statistics.
Best use case
ATACseq-QC is best used when you need a repeatable AI agent workflow instead of a one-off prompt.
Performs ATAC-specific biological validation. It calculates metrics unique to chromatin accessibility assays, such as TSS enrichment scores and fragment size distributions (nucleosome banding patterns). Use this skill when you have filtered BAM file and have called peak for the file. Do NOT use this skill for ChIP-seq data or general alignment statistics.
Teams using ATACseq-QC should expect a more consistent output, faster repeated execution, less prompt rewriting.
When to use this skill
- You want a reusable workflow that can be run more than once with consistent structure.
When not to use this skill
- You only need a quick one-off answer and do not need a reusable workflow.
- You cannot install or maintain the underlying files, dependencies, or repository context.
Installation
Claude Code / Cursor / Codex
Manual Installation
- Download SKILL.md from GitHub
- Place it in
.claude/skills/4-atacseq-qc/SKILL.mdinside your project - Restart your AI agent — it will auto-discover the skill
How ATACseq-QC Compares
| Feature / Agent | ATACseq-QC | Standard Approach |
|---|---|---|
| Platform Support | Not specified | Limited / Varies |
| Context Awareness | High | Baseline |
| Installation Complexity | Unknown | N/A |
Frequently Asked Questions
What does this skill do?
Performs ATAC-specific biological validation. It calculates metrics unique to chromatin accessibility assays, such as TSS enrichment scores and fragment size distributions (nucleosome banding patterns). Use this skill when you have filtered BAM file and have called peak for the file. Do NOT use this skill for ChIP-seq data or general alignment statistics.
Where can I find the source code?
You can find the source code on GitHub using the link provided at the top of the page.
SKILL.md Source
# 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.refRelated Skills
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