I have a bed file of interest that I want to compare with a bigwig file to get the coverage. To do that, I am using deepTools
multiBigwigSummary BED-file -b Norm -out promoter_coverage.zip --BED file.BED --outRawCounts coverage
I want to calculate the coverage over the promoter region (-30 bp to 300bp arround TSS) and I was thinking in the best way to do that. First I thought that it could be possible address this issue editing the bed file as follow
chr start end chr start end (= start +300) chr1 14362 29370 ---> chr1 14362 14662
And for the gen body (if I want a window from 300 bp to the end) :
chr start end chr start (+300) end chr1 14362 29370 ---> chr1 1736 29370
Have this approach any sense? or does anybody knows another better?