Question: Splicing programs to find alternative polyadenylation
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gravatar for kiminsigne
4.4 years ago by
kiminsigne0
United States
kiminsigne0 wrote:

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! 

ADD COMMENTlink modified 3.6 years ago by A. Domingues2.1k • written 4.4 years ago by kiminsigne0
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gravatar for Kirill
3.6 years ago by
Kirill260
Australia
Kirill260 wrote:

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 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.

Cheers

ADD COMMENTlink written 3.6 years ago by Kirill260
0
gravatar for A. Domingues
3.6 years ago by
A. Domingues2.1k
Mainz, Germany
A. Domingues2.1k wrote:

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. 

ADD COMMENTlink written 3.6 years ago by A. Domingues2.1k
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