Hello Simon,

I appreciate your assistance.  A follow-up question: what is the
appropriate method to handle a read that splits an exon junction and is
therefore mapped to two exons when using a short read mapping software?
 Counting it as being present in both exons seems to give undue weight to
the read when using DESeq; conversely, it seems important to "double count"
it when using DEXSeq.  Any advice?  And any software to readily generate
these kinds of files, the matrix files required for DE(X)Seq?  I have just
been using an overlapper script that I wrote using the bam files and ucsc
gene annotations.

Cheers,

Kevin



On Thu, Apr 25, 2013 at 3:29 PM, Simon Anders <anders@embl.de> wrote:

> Hi Kevin
>
>
>  One possible approach is to use reads that fall within any annotated exon
>> as being part of a gene.  And using those measures to normalize and test
>> for differential expression.  And in parallel use DEXSeq to test for
>> differential exon usage.  Does this seem like a reasonable approach?  Any
>> further advice?
>>
>
> As one of the author of both DESeq and DEXSeq, I probably cannot give you
> an unbiased opinion on how our tools compare to cuffdiff; but if you go for
> our methods, then yes, what you wrote is the approach we recommend.
>
>   Simon
>
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-- 
Kevin Lee
Georgia Institute of Technology
Department of Biology
PhD candidate in Bioinformatics

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