Question: Question about HOMER peak annotation to some features. Customize gff3?
gravatar for nanoide
14 months ago by
nanoide50 wrote:

Hi all

So I'm currently annotating some ChIP-seq peaks using HOMER and a gff3 file with the features for my organisms. It seems to be working fine. The features that HOMER is annotating are: "TTS", "Exon", "Intron", "Intergenic" and "Promoter-TSS". But the column of Detailed Annotation is empty. And checking the official webpage here I see there are other features I could be getting, such as "TSS" or "5'UTR Exon".

I would like to get a more precise annotation. For example, my organism has 5'UTR regions annotated, how could I incorporate these ones so I can get also 5'UTR or TSS annotations with HOMER? Maybe I have to change something on my default gff3 or some HOMER parameters? Or HOMER is masking these features with others, maybe expecting the gff3 in some particular format to get Detailed Annotation...

Any advice would be appreciated, thanks

annotation chip-seq homer • 344 views
ADD COMMENTlink modified 14 months ago • written 14 months ago by nanoide50
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1191 users visited in the last hour