> ## Documentation Index
> Fetch the complete documentation index at: https://kalarislabs.com/llms.txt
> Use this file to discover all available pages before exploring further.

# deeptools — AI agent skill for life sciences

> Runs deepTools command-line programs on NGS alignment data: bamCoverage and bamCompare for BAM to bigWig/bedGraph with RPGC, CPM, RPKM or BPM normalizatio…

# `deeptools`

> Runs deepTools command-line programs on NGS alignment data: bamCoverage and bamCompare for BAM to bigWig/bedGraph with RPGC, CPM, RPKM or BPM normalization, multiBamSummary with plotCorrelation and plotPCA, plotFingerprint, computeMatrix with plotHeatmap and plotProfile, and alignmentSieve with --ATACshift. Use when converting BAM files to normalized coverage tracks. Use when checking ChIP-seq quality or comparing replicates. Use when plotting signal around TSS or peak regions. Use when comparing treatment versus control samples. Use when building ChIP-seq, RNA-seq or ATAC-seq coverage workflows. Not for peak calling or differential expression analysis.

**Category:** [life-sciences](/skills#life-sciences) · **License:** BSD license · **Version:** 1.3

## Install

```bash theme={null}
npx research-agent-skills install deeptools
npx skills add KalarisLabs/research-agent-skills --skill deeptools
```

## When to use it

Runs deepTools command-line programs on NGS alignment data: bamCoverage and bamCompare for BAM to bigWig/bedGraph with RPGC, CPM, RPKM or BPM normalization, multiBamSummary with plotCorrelation and plotPCA, plotFingerprint, computeMatrix with plotHeatmap and plotProfile, and alignmentSieve with --ATACshift. Use when converting BAM files to normalized coverage tracks. Use when checking ChIP-seq quality or comparing replicates. Use when plotting signal around TSS or peak regions. Use when comparing treatment versus control samples. Use when building ChIP-seq, RNA-seq or ATAC-seq coverage workflows. Not for peak calling or differential expression analysis.

## Full playbook

Read [SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/main/skills/deeptools/SKILL.md) for the complete workflow, references and any scripts. The agent installer copies the full skill folder.