deepTools — NGS Data Analysis Toolkit

Overview

deepTools is a command-line toolkit for processing and visualizing high-throughput sequencing data. It converts BAM alignments to normalized coverage tracks (bigWig), performs quality control (correlation, PCA, fingerprint), and generates publication-quality heatmaps and profile plots around genomic features. Supports ChIP-seq, RNA-seq, ATAC-seq, and MNase-seq.

When to Use

• Converting BAM files to normalized bigWig coverage tracks
• Comparing ChIP-seq treatment vs input control (log2 ratio tracks)
• Assessing sample quality: replicate correlation, PCA, coverage depth
• Evaluating ChIP enrichment strength (fingerprint plots)
• Creating heatmaps and profile plots around TSS, peaks, or other genomic regions
• Analyzing ATAC-seq data with Tn5 offset correction
• Generating strand-specific RNA-seq coverage tracks
• Use omics-plotting SKILL for custom figures from exported score matrices; standard signal heatmaps/profiles use deeptools' own plotHeatmap/plotProfile
• For read alignment, use STAR, BWA, or bowtie2 instead
• For peak calling, use MACS2 or HOMER instead
• For BAM/VCF file manipulation, use pysam instead

Prerequisites

pip install deeptools
# Verify installation
bamCoverage --version

Input requirements: BAM files must be sorted and indexed (.bai file present). Generate index with samtools index input.bam. BED files for genomic regions (genes, peaks) in standard 3+ column format.

Pre-flight Interview

Settle these with the user before writing any analysis code.

decisions:
  - id: D1
    param: normalizationMethod
    kind: required
    source: user
    ask: "How should coverage be scaled so tracks from different samples can be compared - by read depth, by genome coverage, or not at all?"
    default: "none - raw coverage, comparable only within one sample"

  - id: D2
    param: effectiveGenomeSize
    kind: derived
    source: upstream
    depends_on: [D1]
    ask: "Which assembly's mappable size should the coverage normalization use?"
    default: "looked up for the alignment reference"
    skip_if: "normalization does not require a genome size"

  - id: D3
    param: readExtension
    kind: required
    source: user
    ask: "Should reads be extended to the sequenced fragment length? Correct for ChIP and ATAC, wrong for spliced RNA."
    default: "not extended"

  - id: D4
    param: duplicateHandling
    kind: required
    source: user
    ask: "Should reads flagged as duplicates be ignored when building coverage?"
    default: "included"

  - id: D5
    param: mappingQualityFloor
    kind: required
    source: user
    ask: "Below what mapping confidence should reads be excluded from the signal?"
    default: "no filter"

  - id: D6
    param: binSize
    kind: optional
    source: user
    ask: "At what resolution should signal be summarized?"
    default: "50 bp"

  - id: D7
    param: comparisonOperation
    kind: optional
    source: user
    ask: "When comparing two samples, should the track hold a log ratio, a plain ratio, or a difference?"
    default: "log2 ratio"

  - id: D8
    param: profileAnchor
    kind: optional
    source: user
    ask: "Should profiles be anchored on feature starts, ends, centres, or scaled across whole features?"
    default: "feature start, 500 bp either side"

  - id: D9
    param: processors
    kind: never_ask
    source: data
    reason: "Affects runtime only, not the signal"
    default: "min(8, available_cores)"

D1 and D3 are the pair that makes tracks comparable or quietly misleading. Unnormalized tracks put the deeper-sequenced sample higher everywhere, which reads as biology on a genome browser; extending RNA-seq reads to a fragment length fills introns with signal that was never sequenced.

Quick Start

# Convert BAM to normalized bigWig
bamCoverage --bam sample.bam --outFileName sample.bw \
    --normalizeUsing RPGC --effectiveGenomeSize 2913022398 \
    --binSize 10 --numberOfProcessors 8

# Create heatmap around TSS
computeMatrix reference-point -S sample.bw -R genes.bed \
    -b 3000 -a 3000 --referencePoint TSS -o matrix.gz
plotHeatmap -m matrix.gz -o heatmap.png --colorMap RdBu

Core API

1. BAM to Coverage Conversion

Convert BAM alignments to normalized coverage tracks (bigWig or bedGraph).

# Basic conversion with RPGC normalization
bamCoverage --bam input.bam --outFileName output.bw \
    --normalizeUsing RPGC --effectiveGenomeSize 2913022398 \
    --binSize 10 --numberOfProcessors 8 \
    --extendReads 200 --ignoreDuplicates

# CPM normalization (simpler, no genome size needed)
bamCoverage --bam input.bam --outFileName output.bw \
    --normalizeUsing CPM --binSize 10 -p 8

# RNA-seq: strand-specific coverage
bamCoverage --bam rnaseq.bam --outFileName forward.bw \
    --filterRNAstrand forward --normalizeUsing CPM -p 8
# IMPORTANT: Never use --extendReads for RNA-seq (spans splice junctions)

2. Sample Comparison

Compare treatment vs control or generate ratio tracks.

# Log2 ratio: treatment / control
bamCompare -b1 treatment.bam -b2 control.bam -o log2ratio.bw \
    --operation log2 --scaleFactorsMethod readCount \
    --extendReads 200 -p 8

# Subtract control from treatment
bamCompare -b1 treatment.bam -b2 control.bam -o subtract.bw \
    --operation subtract --scaleFactorsMethod readCount

3. Quality Control

Assess sample quality, replicate concordance, and enrichment strength.

# Sample correlation heatmap
multiBamSummary bins --bamfiles rep1.bam rep2.bam rep3.bam \
    -o counts.npz --binSize 10000 -p 8
plotCorrelation -in counts.npz --corMethod pearson \
    --whatToShow heatmap -o correlation.png
# Good: replicates cluster with r > 0.9

# PCA of samples
plotPCA -in counts.npz -o pca.png --plotTitle "Sample PCA"

# ChIP enrichment fingerprint
plotFingerprint -b input.bam chip.bam -o fingerprint.png \
    --extendReads 200 --ignoreDuplicates
# Good ChIP: steep rise curve; flat diagonal = poor enrichment

# Coverage depth assessment
plotCoverage -b sample.bam -o coverage.png --ignoreDuplicates -p 8

# Fragment size distribution (paired-end)
bamPEFragmentSize -b sample.bam -o fragsize.png

4. Heatmaps and Profile Plots

Visualize signal around genomic features (TSS, peaks, gene bodies).

# Reference-point mode: signal around TSS
computeMatrix reference-point -S chip.bw -R genes.bed \
    -b 3000 -a 3000 --referencePoint TSS -o matrix.gz -p 8

# Scale-regions mode: signal across gene bodies
computeMatrix scale-regions -S chip.bw -R genes.bed \
    -b 1000 -a 1000 --regionBodyLength 5000 -o matrix.gz -p 8

# Generate heatmap
plotHeatmap -m matrix.gz -o heatmap.png \
    --colorMap RdBu --kmeans 3 --sortUsing mean

# Generate profile plot
plotProfile -m matrix.gz -o profile.png \
    --plotType lines --colors blue red

# Multiple signal files: compare marks
computeMatrix reference-point -S h3k4me3.bw h3k27me3.bw -R genes.bed \
    -b 3000 -a 3000 --referencePoint TSS -o multi_matrix.gz
plotHeatmap -m multi_matrix.gz -o multi_heatmap.png

5. Read Filtering and Processing

Filter reads before analysis or correct for assay-specific biases.

# Filter by mapping quality and fragment size
alignmentSieve --bam input.bam --outFile filtered.bam \
    --minMappingQuality 10 --minFragmentLength 150 \
    --maxFragmentLength 700

# ATAC-seq: apply Tn5 offset correction (+4/-5 bp shift)
alignmentSieve --bam atac.bam --outFile shifted.bam --ATACshift
# Then index: samtools index shifted.bam

# GC bias correction (only if significant bias detected)
computeGCBias -b input.bam --effectiveGenomeSize 2913022398 \
    -g genome.2bit --GCbiasFrequenciesFile gc_freq.txt -p 8
correctGCBias -b input.bam --effectiveGenomeSize 2913022398 \
    --GCbiasFrequenciesFile gc_freq.txt -o corrected.bam

6. Enrichment Analysis

Quantify signal enrichment at specific regions.

# Signal enrichment at peak regions
plotEnrichment -b chip.bam input.bam --BED peaks.bed \
    -o enrichment.png --ignoreDuplicates -p 8

Key Concepts

Normalization Methods

Method	Formula	When to Use	Requires
RPGC	1× genome coverage	ChIP-seq, ATAC-seq	--effectiveGenomeSize
CPM	Counts per million	Any assay, quick comparison	Nothing
RPKM	Per kb per million	RNA-seq gene-level	Nothing
BPM	Bins per million	Similar to CPM	Nothing
None	Raw counts	Not recommended for comparison	Nothing

Rule: Use RPGC for ChIP-seq/ATAC-seq (accounts for genome size). Use CPM for quick comparisons. Use RPKM for RNA-seq gene-level analysis.

Effective Genome Sizes

Organism	Assembly	Effective Size
Human	GRCh38/hg38	2,913,022,398
Mouse	GRCm38/mm10	2,652,783,500
Zebrafish	GRCz11	1,368,780,147
Drosophila	dm6	142,573,017
C. elegans	ce10/ce11	100,286,401

computeMatrix Modes

Mode	Use When	Key Params
reference-point	Signal around a fixed point (TSS, peak summit)	-b, -a, --referencePoint
scale-regions	Signal across variable-length features (gene bodies)	-b, -a, --regionBodyLength

Common Workflows

Workflow: ChIP-seq QC and Visualization

#!/bin/bash
# Complete ChIP-seq QC + visualization pipeline
CHIP="chip.bam"
INPUT="input.bam"
GENES="genes.bed"
PEAKS="peaks.bed"
GSIZE=2913022398
THREADS=8

# 1. QC: sample correlation
multiBamSummary bins --bamfiles $INPUT $CHIP -o summary.npz -p $THREADS
plotCorrelation -in summary.npz --corMethod pearson --whatToShow heatmap -o correlation.png

# 2. QC: enrichment fingerprint
plotFingerprint -b $INPUT $CHIP -o fingerprint.png --extendReads 200 --ignoreDuplicates

# 3. Convert to normalized bigWig
bamCoverage --bam $CHIP --outFileName chip.bw --normalizeUsing RPGC \
    --effectiveGenomeSize $GSIZE --extendReads 200 --ignoreDuplicates -p $THREADS

# 4. Log2 ratio track
bamCompare -b1 $CHIP -b2 $INPUT -o log2ratio.bw --operation log2 \
    --scaleFactorsMethod readCount --extendReads 200 -p $THREADS

# 5. Heatmap at TSS
computeMatrix reference-point -S chip.bw log2ratio.bw -R $GENES \
    -b 3000 -a 3000 --referencePoint TSS -o tss_matrix.gz -p $THREADS
plotHeatmap -m tss_matrix.gz -o tss_heatmap.png --colorMap RdBu --kmeans 3

# 6. Profile at peaks
computeMatrix reference-point -S chip.bw -R $PEAKS \
    -b 2000 -a 2000 -o peak_matrix.gz -p $THREADS
plotProfile -m peak_matrix.gz -o peak_profile.png

Workflow: ATAC-seq Analysis

#!/bin/bash
ATAC="atac.bam"
PEAKS="atac_peaks.bed"
GSIZE=2913022398
THREADS=8

# 1. Apply Tn5 offset correction (+4/-5 bp)
alignmentSieve --bam $ATAC --outFile shifted.bam --ATACshift -p $THREADS
samtools index shifted.bam

# 2. Generate RPGC-normalized coverage
bamCoverage --bam shifted.bam --outFileName atac.bw \
    --normalizeUsing RPGC --effectiveGenomeSize $GSIZE \
    --binSize 5 --extendReads -p $THREADS

# 3. Check nucleosome periodicity (expect 200bp/400bp peaks)
bamPEFragmentSize -b shifted.bam -o fragsize.png \
    --maxFragmentLength 1000 --binSize 1

# 4. Heatmap at ATAC peaks
computeMatrix reference-point -S atac.bw -R $PEAKS \
    -b 2000 -a 2000 -o atac_matrix.gz -p $THREADS
plotHeatmap -m atac_matrix.gz -o atac_heatmap.png --colorMap Blues --kmeans 2

Key Parameters

Parameter	Tool(s)	Default	Range	Effect
--normalizeUsing	bamCoverage, bamCompare	None	RPGC, CPM, RPKM, BPM, None	Coverage normalization method
--effectiveGenomeSize	bamCoverage, bamCompare	—	See table above	Required for RPGC normalization
--binSize	bamCoverage, multiBamSummary	50	1–10000	Resolution in bp; smaller = larger files
--extendReads	bamCoverage, bamCompare	False	integer (bp)	Extend to fragment length (ChIP: YES, RNA: NO)
--ignoreDuplicates	Most tools	False	True/False	Remove PCR duplicates
--numberOfProcessors	Most tools	1	1–N cores	Parallel processing
--operation	bamCompare	log2	log2, ratio, subtract, add, mean, reciprocal_ratio	Sample comparison operation
--referencePoint	computeMatrix	TSS	TSS, TES, center	Anchor point for reference-point mode
-b / -a	computeMatrix	500	100–10000 bp	Upstream/downstream distance from reference
--kmeans	plotHeatmap	None	1–20	Number of clusters for heatmap rows
--minMappingQuality	Most tools	None	0–60	Minimum alignment quality filter

Best Practices

1. Always extend reads for ChIP-seq: Use --extendReads 200 (or actual fragment length) — ChIP fragments are longer than reads.

2. Never extend reads for RNA-seq: --extendReads would span splice junctions, creating artifacts.

3. Anti-pattern — comparing with different normalizations: Always use the same normalization method across all samples in a comparison.

4. Use --region for parameter testing: Test on a single chromosome (--region chr1:1-10000000) before running on the full genome — saves hours.

5. Always use --numberOfProcessors: Most tools parallelize well — use all available cores.

6. Anti-pattern — using RPGC without --effectiveGenomeSize: Will silently produce wrong results. Always specify the correct genome size.

7. Run QC before analysis: Check fingerprint and correlation before investing time in heatmaps/profiles. Poor enrichment means downstream visualizations will be noise.

Common Recipes

Recipe: Multi-Sample Correlation Matrix

# Compare 6 samples across the genome
multiBamSummary bins --bamfiles sample{1..6}.bam \
    -o all_samples.npz --binSize 10000 -p 8 \
    --labels S1 S2 S3 S4 S5 S6

# Pearson correlation heatmap
plotCorrelation -in all_samples.npz --corMethod pearson \
    --whatToShow heatmap -o pearson_corr.png --plotNumbers

# Spearman correlation + PCA
plotCorrelation -in all_samples.npz --corMethod spearman \
    --whatToShow heatmap -o spearman_corr.png
plotPCA -in all_samples.npz -o pca.png

Recipe: Gene Body Coverage Profile

# Scale-regions mode for gene body analysis
computeMatrix scale-regions -S sample.bw -R genes.bed \
    -b 1000 -a 1000 --regionBodyLength 5000 -o gene_body.gz -p 8
plotProfile -m gene_body.gz -o gene_body_profile.png \
    --plotType lines --perGroup

Troubleshooting

Problem	Cause	Solution
BAM index not found	Missing .bai file	Run samtools index input.bam
Out of memory	Large genome, small bin size	Increase --binSize; process with --region chr1
Very slow processing	Single-threaded execution	Add -p 8 (or available cores)
bigWig files very large	Bin size too small	Increase --binSize 50 or larger
Flat ChIP fingerprint	Poor ChIP enrichment	Biological issue — consider repeating ChIP experiment
RNA-seq artifacts at exon boundaries	--extendReads used with RNA-seq	Remove --extendReads for RNA-seq data
ATAC-seq signal offset	Missing Tn5 correction	Apply alignmentSieve --ATACshift before analysis
Mismatched genome assemblies	BAM and BED use different assemblies	Verify both use same genome build (hg38 vs hg19)

Related Skills

• pysam-genomic-files — programmatic BAM/VCF manipulation for custom filtering before deepTools
• matplotlib-scientific-plotting — customize deepTools output figures beyond built-in options

References

• deepTools documentation — official user guide and tool reference
• deepTools Galaxy — web-based interface
• Ramirez et al. (2016) "deepTools2: a next generation web server for deep-sequencing data analysis" — Nucleic Acids Research