[BioC] htseq and dexseq

[Steve Lianoglou]

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