Hi, I want to generate an heatmap with peak intensity values for genomic regions.

I'm using the 'computeMatrix' followed by 'plotHeatmap' from 'deeptools'.

MACS2 outputs 3 bedGraph files: 'treat_pileup.bdg', 'control_lambda.bdg' and 'qvalue.bdg', all them i converted to bigWig. Which of those bigWig files should we use in computeMatrix? Which of those shows peak intensity as difference from ChIP and Input?

computeMatrix reference-point -S intensity.bw -R regions.bed -out output.gz --referencePoint center --outFileSortedRegions sortedreg.bed -b 4000 -a 4000 --missingDataAsZero

plotHeatmap -m output.gz -out figure.eps --dpi 300 --colorList '#FFFFFF,#FDF0E3,#FCE1C7,#FBD3AB,#FAC48F,#F8B573,#F7A757,#F6983B,#F58A20' --dpi 300 --whatToShow 'heatmap only' --refPointLabel 'Peak center'