How select top enriched regions from plotHeatmap outputs?

Question

[star]

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 --outFileSortedRegions and --outFileNameMatrix outputs from computeMatrix and plotHeatmap functions. I tried to select a subset based on the top 1000 regions from --outFileSortedRegions.

Answer 1

[kashiff007]

Your default gz file from -o will have full matrix. Sort this file after uncompressing and select the top 1000. It also depend on which region you want to look, this file is matrix of rows where each row corresponds to each each gene (region). If you want to look the enrich region at center of the peak then I suggest take 5 to 10 (depending on how big you took the bin size) central part of the matrix file and calculate the mean, and then sort.