[BioC] Annotation different expressed exon. results from DESeq

[Alejandro Reyes]

Hi Jose,

Thanks for your input, will definitely add it to the "to do" list.

There are things around BioC, like SplicingGraphs, I will have a closer 
look to the recent updates and think how to integrate DEXSeq results 
with this and other packages.

Bests regards,
Alejandro

> 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 at embl.de 
> <mailto:alejandro.reyes at 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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> -- 
> 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 at hsr.it 
> <mailto:garciamanteiga.josemanuel at hsr.it>