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

Alejandro Reyes alejandro.reyes at embl.de
Wed Feb 6 10:06:43 CET 2013


Dear Fong Chun Chan,

Recently I have tried this, and works nicely you just need to count the 
reads falling in the introns and them as "exonic bins" in DEXSeq.

However, I think is recommendable to have strand specific data for this, 
because sometimes intronic regions contain antisense transcripts that if 
they are differentially expressed between your conditions, they can look 
like intron retention differences in your transcripts. Also, when adding 
the introns as "exonic parts" in DEXSeq, the models become big and 
difficult to compute, so it is necessary to use DEXSeq in the TRT 
context (estimateDispersionsTRT and testForDEUTRT).

Best wishes,
Alejandro Reyes



> Hi,
>
> I am interested in trying to detect the intron retention in RNA-Seq I was
> wondering if anyone how ever tried to apply DEXSeq to looking for
> differential intron usage between two groups of samples. It seems like an
> ideal software that could detect for this given that the features are just
> introns now instead of exons. Or does anyone else recommend any other
> Bioconductor package that looks for differential intron retention?
>
> Thanks,
>
> Fong
>
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>
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