Alternative Splicing detection

Question

[xd_d]

Hello all,

I try to find tools to detect AS events like the 5' / 3' extension of a boundary of an exon.

I finde some tools like DSGseq, DEXSeq or Cuffdif,rDiff. And the authors say that you can detect with these tools AS-events.

But I tested that and it seems like DSGseq DEXSeq check only if a exon expressed or not . And Cuffdiff check the different isoforms of samples.

Do I have missunderstand AS-events. ?? Why they say that these tools detect AS-event but it cant.. or do compare expression of different isoforms.

Which tool can idendefind the 5' / 3' extension of a boundary of an exon.

And means differential AS detection methods , a tool to detect AS events or different spliced transcript isoforms ?

Thanks all

Answer 1

[badribio]

I am guessing here, kindly go over these tools and see if it answers your questions..

http://rnaseq-mats.sourceforge.net/

http://genes.mit.edu/burgelab/miso/

Answer 2

[BioNinja]

I think rMATS is what you wanted. rMATS has an extremely fast version(rmats-docker) now. it takes about 10-20 mins to run, much faster than MISO. see here: http://rnaseq-mats.sourceforge.net/rmatsdockerbeta/

[xd_d]

Hey thanks I read the paper: https://www.ncbi.nlm.nih.gov/pubmed/22266656 and they only test if a exon in a transcript or not. But i dont find alternative 5'/3' splicing sites. Do I need a 5' alternative splice annotation file for rMats ?

Answer 3

[Kristoffer Vitting-Seerup]

Tbe R package spliceR can identify and analyze such events based on Cufflinks data.