I used the deeptools to draw plotHeatmap for ChIP-seq peaks across an epigenome mark. Now, I would like to select top (e.g: top1000) enriched regions based on the plotHeatmap to apply Motif analysis on those regions but I am not sure which output can be useful to extract Top regions?
I have both
--outFileNameMatrix outputs from computeMatrix and plotHeatmap functions. I tried to select a subset based on the top 1000 regions from