[BioC] htseq and dexseq

[Steve Lianoglou]

Hi,

On Wed, Jun 26, 2013 at 2:00 PM, Andreia Fonseca
<andreia.fonseca at gmail.com> wrote:
> Thanks Steve,
>
> The vignette looks very useful. ;y question was not related with counting
> into two exons of same gene. With Htseq we get counts for exons that
> overlap different genes, so it creates feature fusing two or more genes,
> and I don't know how to handle this. should I look into the counts of the
> exons of the single gene
> , or of the counts of exons the gene fusions?

Remember that I've never used ht-seq, but I'll assume that it's easy
enough to find the "bins" that result from an exonic region shared
between two different genes.

The way I'd handle these special cases is that I wouldn't handle them
at all and I'd likely prefer to remove those bins from my initial
analysis -- I suspect the number of such cases would be relatively few
when compared to the number of "kosher" bins.

HTH,
-steve

--
Steve Lianoglou
Computational Biologist
Bioinformatics and Computational Biology
Genentech