Hi all, I am working on a project where I need to check H3K79 methylation levels at enhancer sites. I have the enhancer locations as a bed file, I have the wiggle and bed file of methylation ChIP-Seq. Is there a way I can generate a count data out of wiggle format? I am thinking of processing the raw data from the start and get the bam files,with the enhancer bed file I already had, use bedtools to count the reads, then do DESeq2 for differential methylation levels.
If there is an alternative way to do this from wiggle and bed files(both from ENCODE Project) I would save some time from rerunning the alignment for 15 samples.