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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.

plugins/KalarisLabs/research-agent-skills/skills/deeptools/SKILL.md

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Nov 6, 2026
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Apache-2.0

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# deepTools: NGS Data Analysis Toolkit

## Overview

deepTools is a comprehensive suite of Python command-line tools designed for processing and analyzing high-throughput sequencing data. Use deepTools to perform quality control, normalize data, compare samples, and generate publication-quality visualizations for ChIP-seq, RNA-seq, ATAC-seq, MNase-seq, and other NGS experiments.

**Core capabilities:**
- Convert BAM alignments to normalized coverage tracks (bigWig/bedGraph)
- Quality control assessment (fingerprint, correlation, coverage)
- Sample comparison and correlation analysis
- Heatmap and profile plot generation around genomic features
- Enrichment analysis and peak region visualization

## When to Use This Skill