Splicing programs to find alternative polyadenylation

Question

[kiminsigne]

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!

Answer 1

[Dr Reema Singh]

Here's some information

• http://rnaseq.uoregon.edu/
• http://www.rna-seqblog.com/radpre-a-computational-program-for-identification-of-differential-mrna-processing-including-alternative-polyadenylation/
• http://www.nature.com/ncomms/2014/141120/ncomms6274/abs/ncomms6274.html

Answer 2

[Kirill Tsyganov]

Hi Kiminsigne,

I can see its been a while since you've posted this question, but never the less I think you will find this paper 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.

Cheers

Answer 3

[A. Domingues]

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.