htseq-count without GTF?
Entering edit mode
2.1 years ago
blur ▴ 260


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. 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,

FPKM count htseq htseq-count gtf • 808 views
Entering edit mode
2.1 years ago
ATpoint 66k

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


Login before adding your answer.

Traffic: 2563 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6