Peak calling in extended 3'UTR regions

[Matthew Gazzara]

Hi, 

Just wondering how CLIPper behaves with peak calling on RBPs that bind downstream of the cleavage and polyadenylation site of a pre-mRNA (e.g. CSTF2T). 

I know peaks are called on a per-gene basis, but is an extension added to the annotated 3'UTR / polyadenylation site? I'm just wondering if this is done in order to call peaks on such RBPs that normally bind downstream of this site or to handle cellular contexts where an extended 3'UTR may exist in the mRNA. Or instead would this be considered intergenic space and is it possible to call peaks in these regions? 

Thanks for your help with this,

Matthew Gazzara