---
title: "deepTools Quick Reference"
description: "plotHeatmap -m matrix.gz -o heatmap.png ```"
type: skill
canonical_url: https://claudary.paisolsolutions.com/skills/quick-reference-2
source: "Claudary"
difficulty: intermediate
author: "Claude Code Knowledge Pack"
date: 2026-07-10T11:37:26.215Z
license: CC-BY-4.0
attribution: "deepTools Quick Reference — Claudary (https://claudary.paisolsolutions.com/skills/quick-reference-2)"
---

# deepTools Quick Reference
plotHeatmap -m matrix.gz -o heatmap.png ```

## Overview

# deepTools Quick Reference

## Most Common Commands

### BAM to bigWig (normalized)
```bash
bamCoverage --bam input.bam --outFileName output.bw \\
    --normalizeUsing RPGC --effectiveGenomeSize 2913022398 \\
    --binSize 10 --numberOfProcessors 8
```

### Compare two BAM files
```bash
bamCompare -b1 treatment.bam -b2 control.bam -o ratio.bw \\
    --operation log2 --scaleFactorsMethod readCount
```

### Correlation heatmap
```bash
multiBamSummary bins --bamfiles *.bam -o counts.npz
plotCorrelation -in counts.npz --corMethod pearson \\
    --whatToShow heatmap -o correlation.png
```

### Heatmap around TSS
```bash
computeMatrix reference-point -S signal.bw -R genes.bed \\
    -b 3000 -a 3000 --referencePoint TSS -o matrix.gz

plotHeatmap -m matrix.gz -o heatmap.png
```

### ChIP enrichment check
```bash
plotFingerprint -b input.bam chip.bam -o fingerprint.png \\
    --extendReads 200 --ignoreDuplicates
```

## Effective Genome Sizes

| Organism | Assembly | Size |
|----------|----------|------|
| Human | hg38 | 2913022398 |
| Mouse | mm10 | 2652783500 |
| Fly | dm6 | 142573017 |

## Common Normalization Methods

- **RPGC**: 1× genome coverage (requires --effectiveGenomeSize)
- **CPM**: Counts per million (for fixed bins)
- **RPKM**: Reads per kb per million (for genes)

## Typical Workflow

1. **QC**: plotFingerprint, plotCorrelation
2. **Coverage**: bamCoverage with normalization
3. **Comparison**: bamCompare for treatment vs control
4. **Visualization**: computeMatrix → plotHeatmap/plotProfile

---

Source: [Claudary](https://claudary.paisolsolutions.com/skills/quick-reference-2) · https://claudary.paisolsolutions.com