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

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

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

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

plotFingerprint -b input.bam chip.bam -o fingerprint.png \
    --extendReads 200 --ignoreDuplicates