gh-k-dense-ai-claude-scientific-skills-scientific-skills/skills/deeptools/assets/quick_reference.md

deepTools Quick Reference

Most Common Commands

BAM to bigWig (normalized)

bamCoverage --bam input.bam --outFileName output.bw \
    --normalizeUsing RPGC --effectiveGenomeSize 2913022398 \
    --binSize 10 --numberOfProcessors 8

Compare two BAM files

bamCompare -b1 treatment.bam -b2 control.bam -o ratio.bw \
    --operation log2 --scaleFactorsMethod readCount

Correlation heatmap

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

Heatmap around TSS

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

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