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

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

annotation chip-seq homer • 261 views
ADD COMMENTlink modified 10 months ago • written 10 months ago by nanoide50
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