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?

thanks a bunch


On Wed, Jun 26, 2013 at 5:27 PM, Steve Lianoglou
<lianoglou.steve@gene.com>wrote:

> Hi Andreia,
>
> It's hard to parse the read stats you put into the email due to some
> forced wrapping, I guess, so I'm not quite sure what the numbers are
> that you are showing, but you say regarding the htseq counting for
> exons:
>
> > But then the most weird thing is that the total is being much higher
> than the
> > number of reads aligned,
>
> While I've never actually used ht-seq to count for DEXSeq, from the
> chatter on this list I'm pretty sure that it will likely double count
> a read if it spans more than one exon, ie. one exon will assign a +1
> to the count for every exon it spans. If that can explain the issue
> that you are seeing, then this is expected behavior -- and moreover,
> you actually want that.
>
> As an aside, the vignette that comes with the parathyroidSE data
> packge has a section that shows you how to do DEXSeq entirely using
> R/bioconductor tools:
>
>
> http://bioconductor.org/packages/release/data/experiment/vignettes/parathyroidSE/inst/doc/parathyroidSE.pdf
>
> HTH,
>
> -steve
>
> --
> Steve Lianoglou
> Computational Biologist
> Bioinformatics and Computational Biology
> Genentech
>



-- 
---------------------------------------------------------------------------------------------
Andreia J. Amaral, PhD
BioFIG - Center for Biodiversity, Functional and Integrative Genomics
Instituto de Medicina Molecular
University of Lisbon
Tel: +352 217500000 (ext. office: 28253)
email:andreiaamaral@fm.ul.pt ; andreiaamaral@fc.ul.pt

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