Calculating FPKM of reads that overlap regions of interest

Question

[AB]

Hi,

I have the data from a ChIP-Seq experiment. I used deeptools bamCompare on the treatment and input files to get a normalized coverage file in bigwig format which i converted to bed file using BigwigToWig and wig2bed. I have another bed file with the promoter regions I am interested in. i used bedtools compare on both the bed file to get the overlaps. I am interested in the FPKM values and not the counts. Is there some way to compare the bed files and get the FPKM value of each overlapping region of interest ?

[Devon Ryan]

There's really no clear way to go from a bamCompare-derived ratio to FPKMs. What are you actually trying to do?