Hi Alejandro and list,
Since this is a recurrent topic about alternative splicing with RNA-Seq and
the robust DEXSeq software, are you planning to include some 'downstream'
tool to guide on the classification of the AS events based on the bam
alignments? I known there are some tools like splicegrapher.py and other
few out there but it would be a perfect end point for the R/DEXSeq package.
Thanks again
Jose



2014-03-03 9:35 GMT+01:00 Alejandro Reyes <alejandro.reyes@embl.de>:

> Dear Fabrice,
>
> I think you meant DEXSeq.
> To classify events into alternative splicing types it is useful to go
> back to the alignment files and visualize the exon-exon junction reads,
> then it becomes obvious which are the events that are giving rise to the
> differences in exon usage.
>
> Best regards,
> Alejandro
>
>
>
> > Dear list,
> >
> > When I use DESeq find different expressed exon in tow conditions. e.g,
> >
> >     id baseMean  baseMeanA    baseMeanB
> > 1 ENSMUSG00000079102:009 851.0096 1697.09604    4.9231156
> > 2 ENSMUSG00000026727:016 239.6701  478.35562    0.9846231
> > 3 ENSMUSG00000026727:004 155.8972  311.79442    0.0000000
> >
> > How can know the Alternative Splicing Event for
> > ENSMUSG00000079102:009, ENSMUSG00000026727:016 and
> > ENSMUSG00000026727:004?
> > for example, Cassette exon (skipped exon), Intron retention, Mutually
> > exclusive exons, Alternative 3' sites, Alternative 5' sites,
> > Alternative first exon.
> >
> > Thank you very much in advance.
> >
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> >
>
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-- 
Jose M. Garcia Manteiga PhD
Research Assistant - Data Analysis in Functional Genomics
Center for Translational Genomics and BioInformatics
Dibit2-Basilica, 3A3
San Raffaele Scientific Institute
Via Olgettina 58, 20132 Milano (MI), Italy

Tel: +39-02-2643-4751
e-mail: garciamanteiga.josemanuel@hsr.it

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