Calculating FPKM of reads that overlap regions of interest
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 ?
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
bedGraphToBigWig: Missing Genome Coordinates
written by RelativeOptics •
-
peak calling in CUT&RUN(Chipseq) Analysis
written by minoo •
-
Why are there regions missing from mappability tracks provided by UCSC?
written by jparker4 •
-
Signal-Noise Normalization between 2 Chip-Input experiment
written by hiroyuki.kato.911 •
-
Chip-Seq input normalization with deeptools
written by srhic •
-
Removing outliers from bigwig files
written by srhic •
-
Very high negative scores from bigWigAverageOverBed
written by AB
-
What is a good cutoff of mappability score from bigWigAverageOverBed ?
written by AB
-
what do negative values from bigWigAverageOverBed output mean?
written by AB
-
merging two bigwig files
written by ATCG
There's really no clear way to go from a bamCompare-derived ratio to FPKMs. What are you actually trying to do?