[khmer] Preferred aligner

C. Titus Brown ctb at msu.edu
Tue Sep 17 21:06:56 PDT 2013


On Wed, Sep 18, 2013 at 12:13:21AM +0100, Richard Smith wrote:
> Dear Joann,
> 
> I'm not Dr Brown, but we also do a lot of RNAseq on plants, so perhaps I can offer out experience.
> 
> We use either RSEM or eXpress for quantification. The results are almost identical from the two, but eXpress is much faster while RSEM allows you to extract the probabilities for each alignment, so they are each useful in different scenarios. We tend to use Bowtie1 for quantification.
> 
> Richard Smith
> Department of Plant Sciences
> University of Cambridge

Richard, thanks for your response!  Glad your experience supports what
we're hoping to do :)

Joann, we've put together an RSEM tutorial here:

https://khmer-protocols.readthedocs.org/en/latest/mrnaseq/6-comparative-expression-with-rsem.html

but it is buyer-beware.  The other steps in that protocol might also be
interesting, but again, the protocol is still not yet mature.  Comments
very welcome, though.

cheers,
--titus

> > On 17 Sep 2013, at 23:54, Joann Diray Arce <joann.diray at gmail.com> wrote:
> > 
> > Dr. Brown,
> > 
> > I am doing RNA-seq with plants. Do you have any preferred aligner and software that will do abundance estimation?
> > 
> > -Joann Arce
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> > khmer at lists.idyll.org
> > http://lists.idyll.org/listinfo/khmer

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-- 
C. Titus Brown, ctb at msu.edu




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