[BioC] Fwd: Regarding multiple hits of same read

[Steve Lianoglou]

Hi,

On Tue, Sep 24, 2013 at 11:04 AM, deepika lakhwani
<lakhwanideepika at 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