[BioC] htseq and dexseq

[Andreia Fonseca]

here is an attach with the summary of the counts I sent


On Wed, Jun 26, 2013 at 10:00 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?
>
> thanks a bunch
>
>
> On Wed, Jun 26, 2013 at 5:27 PM, Steve Lianoglou <lianoglou.steve at 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 at fm.ul.pt ; andreiaamaral at fc.ul.pt
>



-- 
---------------------------------------------------------------------------------------------
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 at fm.ul.pt ; andreiaamaral at fc.ul.pt