Question about HOMER peak annotation to some features. Customize gff3?

Question

[nanoide]

Hi all

So I'm currently annotating some ChIP-seq peaks using HOMER annotatePeaks.pl 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

Answer 1

[river]

Hi, I came across the same problems. "5'UTR Exon","3'UTR Exon" annotations were missing in the output file. I wonder have you solve the problems?

Answer 2

[nanoide]

Hi, I'm afraid I didn't find the solution. I ended up using other software like Chipseeker, where I found I have more control over the features, the priority...etc