Steve Lianoglou | 3 Oct 17:48 2012
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Re: shan

Hi,

On Wed, Oct 3, 2012 at 9:48 AM, wang peter <wng.peter@...> wrote:
> dear steve:
> you are right,
>
> 1.  51 bp lib is too short for assembly

Does that mean you *need* to do assembly for downstream analysis?

Are you not aligning to a genome? Or do you have a genome, but also
want to do to transcript assembly to identify novel transcripts? Maybe
your genome is poorly annotated? What type of data are you working
with here? Plant? Animal? Which plant/animal, etc ...

I'm not sure what to tell you, partly because you're not giving a lot
of information in your question/answers. You are giving facts about
your data, but no motivation regarding the question you're trying to
answer, and what is stopping you from doing so.

You also say:

> 3 i want to find DE genes between DLCK vs LCK
>
> BUT i donot want to combine 51 bp with 100 bp data, which removing the
> replicate variation
> (DLCK1+DCLK1-51bp       DLCK2....       DLCK3.....) vs ....

OK.

So your analysis twice, once w/ 51bp, and again w/ 100bp -- see how
they compare.

If you need to assemble transcripts first, do so w/ the 100bp reads,
then quantify their expression with each library separately.

--

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

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