[BioC] DESeq versus CuffDiff2 for RNA-seq expression quantification in parasite-infected blood

[Simon Anders]

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