htseq-count without GTF?

Question

[blur]

Hi,

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,

Answer 1

[ATpoint]

Use featureCounts, check its custom SAF format which you can use to count over any genomic position of choice.