deepTools

Overview

deepTools is a suite of Python-based tools for exploring deep-sequencing data. It converts BAM files into normalised coverage tracks (bigWig), computes sample-to-sample correlations, and generates publication-ready heatmaps and profile plots of signal enrichment around genomic features. deepTools is widely used in ChIP-seq, ATAC-seq, and RNA-seq workflows for visual quality control and downstream analysis of read coverage.

Installation

mamba install -c bioconda deeptools

Basic Usage

Generate a normalised coverage track (RPKM)

bamCoverage -b sample.bam -o sample.bw \
  --normalizeUsing RPKM --binSize 10 -p 8

Compute correlation between replicates

multiBamSummary bins -b rep1.bam rep2.bam rep3.bam \
  -o results.npz -p 8
plotCorrelation -in results.npz --corMethod spearman \
  -o correlation_heatmap.pdf --plotFileFormat pdf

Generate a heatmap of signal around TSS

computeMatrix reference-point -S chip.bw input.bw \
  -R genes.bed -a 3000 -b 3000 -o matrix.gz
plotHeatmap -m matrix.gz -o heatmap.pdf

Key Parameters

Flag / option	Description
`-b`	Input BAM file(s).
`-o`	Output file (bigWig, matrix, or plot depending on the sub-command).
`-p THREADS`	Number of processors to use.
`--normalizeUsing`	Normalisation method for `bamCoverage`: `RPKM`, `CPM`, `BPM`, `RPGC`, or `None`.
`--binSize INT`	Length in bases of the output bins (default: 50).
`--effectiveGenomeSize INT`	Mappable genome size, required when using `RPGC` normalisation.
`-S`	Input bigWig score file(s) for `computeMatrix`.
`-R`	BED or GTF file of regions for `computeMatrix`.
`-a / -b`	Distance in bp downstream (`-a`) and upstream (`-b`) of the reference point in `computeMatrix reference-point`.
`--corMethod`	Correlation method for `plotCorrelation`: `spearman` or `pearson`.

Expected Output

bamCoverage – a bigWig (.bw) file containing normalised per-bin coverage values, suitable for genome-browser visualisation.
multiBamSummary – a compressed NumPy archive (.npz) storing the read-count matrix across genomic bins for all input BAM files.
plotCorrelation – a PDF (or PNG/SVG) heatmap or scatterplot showing pairwise sample correlations.
computeMatrix – a gzipped matrix file used as input for plotHeatmap and plotProfile.
plotHeatmap – a PDF (or PNG/SVG) heatmap of signal intensity around the specified genomic features.