I have a genomic alignment for IP vs. input files. I want to count the coverage of an entire feature to do FPKM of the IP vs. input to see if there was an enrichment after IP. The features I want to check are NOT genes, but areas in the genome like promotors, enhancers and so on, There is no GTF for them, I only have a bed file with locations.
I came across the tool htseq-count - it looks like what I need, only I don't have a GTF. https://htseq.readthedocs.io/en/release_0.11.1/count.html I saw a few R packages too, but they too require a GTF.
What can I do? can I run it without? (I checked the manual and didn't see such an option) Is there another way to check?
Thanks for your help,