# deeptools

A skill that turns sequencing data into coverage tracks, QC metrics and heatmaps around TSS and peaks.

- skill · `type=skill` · Claude Code, Codex, Cursor, GitHub Copilot, Gemini CLI, OpenCode · 1900 installs · ★ 54652
- Author: K-Dense-AI
- License: LicenseRef-BSD-license · policy=link-only · description only; the file stays with the author
- Source: https://github.com/K-Dense-AI/scientific-agent-skills/tree/HEAD/skills/deeptools/SKILL.md
- Updated: 2026-10-19
- HTML: https://affpapa.org/en/nevibecode/skills/deeptools

## What it does

The skill hands your agent the deepTools command set for high-throughput sequencing work. It converts BAM alignments into normalized coverage tracks, computes quality metrics, compares samples and draws heatmaps with profiles around genomic features. Reach for it when you need to process ChIP-seq, RNA-seq or ATAC-seq and produce figures for a paper or a report.

Two scripts ship with it: `scripts/validate_files.py` and `scripts/workflow_generator.py`. The first checks local BAM, bigWig and BED files — structure, coordinate order, headers, every BED row. The second builds a runnable script for a standard scenario such as `chipseq_qc`, filling in your file names. Reference notes cover normalization methods, effective genome sizes and per-tool options.

You need Python 3.12+ and deepTools 4.0.0 with pysam and pyBigWig; samtools handles sorting and indexing. Five commands were rewritten in Rust for 4.0.0: `bamCoverage`, `bamCompare` and `multiBamSummary` no longer take `--ignoreDuplicates`, and `--exactScaling` is gone. Pipelines still carrying those flags break at argument parsing, so check your commands before a cluster run.

## Install

### Claude Code (native platform)

1. **Skills CLI (Vercel)**
```bash
npx skills add K-Dense-AI/scientific-agent-skills --skill deeptools -a claude-code
```

2. **Manually: put the files in place**
- File: `~/.claude/skills/deeptools/SKILL.md` — Copy the whole skill folder; for one project use .claude/skills/deeptools/

### Codex

1. **Skills CLI (Vercel)**
```bash
npx skills add K-Dense-AI/scientific-agent-skills --skill deeptools -a codex
```

2. **Manually: put the files in place**
- File: `.agents/skills/deeptools/SKILL.md` — For all projects use ~/.agents/skills/

### Cursor

1. **Skills CLI (Vercel)**
```bash
npx skills add K-Dense-AI/scientific-agent-skills --skill deeptools -a cursor
```

2. **Manually: put the files in place**
- File: `.cursor/skills/deeptools/SKILL.md` — Cursor also reads .agents/skills/ and .claude/skills/

### GitHub Copilot

1. **GitHub CLI**
```bash
gh skill install K-Dense-AI/scientific-agent-skills deeptools
```

2. **Manually: put the files in place**
- File: `.github/skills/deeptools/SKILL.md`

### Gemini CLI

1. **Skills CLI (Vercel)**
```bash
npx skills add K-Dense-AI/scientific-agent-skills --skill deeptools -a gemini-cli
```

2. **Platform CLI**
```bash
gemini skills install https://github.com/K-Dense-AI/scientific-agent-skills --path skills/deeptools
```

### Windsurf (Devin Desktop)

**Manually: put the files in place**
- File: `.devin/skills/deeptools/SKILL.md` — The legacy .windsurf/skills/ path still works

### OpenCode

**Skills CLI (Vercel)**
```bash
npx skills add K-Dense-AI/scientific-agent-skills --skill deeptools -a opencode
```

### Claude.ai

**Claude.ai**
- Zip the folder and upload it in Settings → Capabilities → Skills

Where a file is given instead of a command, copy the files from the source to that path: https://github.com/K-Dense-AI/scientific-agent-skills/tree/HEAD/skills/deeptools/SKILL.md

## When to use it
- convert BAM alignments into normalized bigWig tracks for a genome browser
- check ChIP-seq quality with fingerprints and replicate correlation
- plot a heatmap of signal around TSS or peak regions
- compare treatment against control as a log2 ratio
- generate a runnable script for a standard workflow with your files

## Example prompts
- Validate `sample1.bam` and `regions.bed` with the validation script
- Generate the `chipseq_qc` workflow for `ChIP1.bam` and `ChIP2.bam`
- Compute correlation between replicates and show me the result

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From the same set: [k-dense-ai/scientific-agent-skills](https://affpapa.org/en/nevibecode/by/k-dense-ai/scientific-agent-skills.md) — 159 cards

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