[BioC] htseq and dexseq
Steve Lianoglou
lianoglou.steve at gene.com
Wed Jun 26 18:27:27 CEST 2013
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
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