Thank You Steve...


On Wed, Sep 25, 2013 at 12:35 AM, Steve Lianoglou
<lianoglou.steve@gene.com>wrote:

> Hi,
>
> On Tue, Sep 24, 2013 at 11:04 AM, deepika lakhwani
> <lakhwanideepika@gmail.com> wrote:
> > Thank You...Steve for answering.
> >
> > Ok...I am reading all the pdfs very carefully and I am satisfy with your
> > answer.
> > But please clear my some basic question...
> > which type of reads are selected in differential expression analysis?
> > I understand that only unique mapped reads use for differential
> expression
> > analysis but I think multimapped reads also have an important role
> > in differential expression analysis because genome has so many
> > duplicated/paralogous genes. if I am wrong then please tell me.
>
> You are not wrong, multimapped reads are obviously important since
> they are "real" -- ie. they are transcribed from somewhere, and if you
> could know exactly where it would be a good thing.
>
> It is still an open question as to how to use them best. Although I
> haven't used it myself, RSEM comes up often enough that it seems like
> many people think its use is a good idea, so you can start there:
>
> http://www.biomedcentral.com/1471-2105/12/323
>
> Using the references there as a seed to do a more thorough literature
> search and finding papers that cite RSEM should be helpful, as well as
> your "normal" google searching mojo.
>
>
> HTH,
> -steve
>
> --
> Steve Lianoglou
> Computational Biologist
> Bioinformatics and Computational Biology
> Genentech
>

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