[BioC] Detecting differential usage of introns from RNA-seq data.

[Alejandro Reyes]

Dear Delasa Aghamirzaie,

I did this once and it worked fine. Just make sure you have strand 
specific data or to have a close look at your hits (you might confound 
your hits with any kind of antisense transcripts differentially 
expressed).  The DEXSeq python scripts should do the job (also allowing 
counting those reads that fall partially in an exon or an intron), you 
just need to add to the "flattened annotation file" the information 
about your introns.

Best regards,
Alejandro

> Hi Alejandro,
>
> I was reading the messages between you and Fong for testing differential
> intron usage.  I am interested in finding intron retention events in my
> data as well, since intron retention is the most frequent splicing event in
> plants rather than exon skipping. I have already did DEXSeq for
> differential exon usage. I was wondering if in preprocessing step, I should
> count the reads falling into introns using "dexseq_count.py" and
> "dexseq_prepare_annotation.py"? GTF files usually does not have information
> about Introns, should I add this information manually? Another question is
> that should I count reads falling into exons as well as introns to get
> intron retention events? Thanks
>
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>
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