Question: Calculating FPKM of reads that overlap regions of interest
gravatar for Apoorva
4.4 years ago by
United States
Apoorva270 wrote:


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 ?

chip-seq fpkm bedtools • 1.8k views
ADD COMMENTlink written 4.4 years ago by Apoorva270

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

ADD REPLYlink written 4.4 years ago by Devon Ryan98k
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