[BioC] need help for the study design of a RNA-Seq project

[Moritz Hess]

Hi Shirley,

I would say it depends. If you are investigating an organism with no good
transcriptomic or genomic sequence ressources, I would also recommend 100bp
PE because for a subsequent assembly of the reads this is for shure
beneficial. If you have plenty of genomic ressources available, I would not
generally discard the 50bp option. I attached a paper that partially covers
the length / precision debate. Maybe it is helpful for you.

Best regards

Moritz

2013/4/12 shirley zhang <shirley0818 at gmail.com>

> Dear Wei, Sean and Dario,
>
> Many thanks for all of your reply and suggestions. I really appreciate.
>
> I will check the ENCODE RNA-seq guidelines.I also posted my question at
> Biostars.
>
> Thanks again,
> Shirley
> On Thu, Apr 11, 2013 at 9:59 PM, Dario Strbenac <d.strbenac at garvan.org.au
> >wrote:
>
> > It is a question to ask at Biostars which has the address
> > http://www.biostars.org/
>
>
>
> <zhangxl at bu.edu>
>
>         [[alternative HTML version deleted]]
>
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-- 

*Moritz Heß
PhD Candidate
*
*Research associate
Forest Research Institute
of Baden Württemberg (FVA)
Wonnhalde 4
79100 Freiburg (Germany)

phone +49 761 4018 301*
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