I'm working with RNA-seq data and I'm trying to find a very specific splice form of a certain gene and the type of splicing is alternative polyadenylation. I've been working with MATS and Olego/Quantas but as stated in their documentation, they only look for skipped/cassette exons, alternative 5' splice sites, alternative 3' splice sites, mutually exclusive exons, and retained introns. Does anyone know of a program I can use to specifically look for alternative polyadenylation splicing? Or if there is a quick fix to modify these other programs to look for it? Thanks!
Here's some information
I can see its been a while since you've posted this question, but never the less I think you will find this paper http://rnajournal.cshlp.org/content/21/8/1502.long rather useful. Just in case link is broken here is the name of the paper PAT-seq: a method to study the integration of 3' -UTR dynamics with gene expression in the eukaryotic transcriptome. This paper should lead you to tail-tools, which might be useful for you.
I have tried isoSCM and it worked pretty well. For a number of reasons we don't have lab validation of the results, but on IGV things looked OK. The output is also pretty easy to understand and analyse.