How to plot heatmap is of ATAC-seq sites at gene promoters

[Krithika-Bhuvan]

Dear Deeptools authors,

I'm looking for some advice. I'm looking to plot a heatmap similar to panel D in this figure: https://ars.els-cdn.com/content/image/1-s2.0-S2211124720302989-gr1_lrg.jpg The signal on the top panel (the “grey colored mountains” ) have the label “genes”.

The author said the heatmap is of ATAC-seq sites at gene promoters. They annotated the peaks to genes, and plotted sites in the promoter. The top panel of the heatmap is the the average signal of the heatmap (at lest they think the average is the default).

I'm unsure what information used as the bed file and what was used as bigwig file in order to get this plot. Would you be able to advice me ? Thank you

Possible steps ?

• Save the diff peak regions in the ATAC as a bed file
• Annotate the diff peak regions to connect ATAC regions to genes. Subset those genes in promoter regions.
• Should i save the FPKM gene expression data of those genes as bigwig file ????