I have some bigWig files downloaded from the Encode project for specific ChiP-Seq data of human genome.
I would like to somehow extract the genes, which overlap the regions in these bigWig files.
I know I can convert the bigWig files into Bedgraph using the UCSC tools and I have also found bwtools on Github which can also manipulates bigwig files (into bed too).
but What do I do next?
How do I compare the resulted bed (or Bedgraph) file with my annotation files?
Does anyone has an idea as to how this can be done?
thanks in advance