[BioC] DESeq and transcript-wise analysis

[Nicolas Delhomme]

Dear Abhi,

If you could point me to some published strand specific data or let me get an excerpt of yours, I could easily had strand-specificity in the easyRNASeq package.

Thanks,

Nico

---------------------------------------------------------------
Nicolas Delhomme

Genome Biology Computational Support

European Molecular Biology Laboratory

Tel: +49 6221 387 8310
Email: nicolas.delhomme at embl.de
Meyerhofstrasse 1 - Postfach 10.2209
69102 Heidelberg, Germany
---------------------------------------------------------------





On 9 Feb 2012, at 00:41, Abhishek Pratap wrote:

> Hi Elena
> 
> Good timing with me on this. I recently was contemplating the best way
> to move forward for a similar analysis. HTSeq  a python based toolkit
> by Simon can help you do the counting.  FYI : It can also take strand
> info into account.  If you dont have stranded data you could also look
> at easyrnaseq package.
> 
> So if you have an annotation file like gff/gtf with the isoform
> information you could then do the read counting at isoform or gene
> level based on which attribute of the gff file you select to do the
> counting. Check out
> http://www-huber.embl.de/users/anders/HTSeq/doc/count.html.
> 
> Also you want to keep in mind that at isoform level you would be
> double counting the reads in exons which are shared in the isoforms
> which can bias your results to some extent. But as Wolfgang pointed
> out in a recent post if you use FDR, it should not matter a lost as
> the bias will be cancelled between denominator /numerator.
> 
> You also might want to check the DEXSeq which can help infer
> differential expression from RNA-Seq exons which could then be related
> back to genes/isoforms.
> 
> Hope this helps and let us know about your progress. I would be
> interested in learning from your experience too.
> 
> Cheers!
> -Abhi
> 
> ----------------------------------
> Abhishek Pratap
> Bioinformatics Systems Analyst - 3
> DOE- Joint Genome Institute
> Lawrence Berkeley National Lab
> 
> 
> 
> 
> On Wed, Feb 8, 2012 at 3:26 PM, Elena Sorokin <sorokin at wisc.edu> wrote:
>> Greetings all,
>> 
>> After re-reading related posts in the listserv archive, I still didn't know
>> the exact answer to my question, so here goes. I'd like to use DESeq to
>> measure differential isoform expression. Has Simon or anybody else written a
>> script that will convert aligned reads (.bam/.sam file) into a table of
>> isoform counts, suitable for input to DESEq - similar to what Simon has done
>> at the gene-wise level, but instead for making a table of counts by isoform?
>> 
>> I would try to do this myself, but I'm a novice at programming. Sorry if
>> this has been answered elsewhere... If so, please let me know the link.
>> 
>> Thanks,
>> Elena
>> 
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