Dear Moritz,

Thanks a lot for your suggestions and circulating the paper. I will read it.

Sorry that I forgot to mention in my original question. We are working on
human samples.

During the design, the RNA fragment size has to be taken into account as
well. If the fragment is 150-200bp, then 100 paired end is a waste as the
reads will frequently overlap. Am I right? So I might go to option 2 (76bp
PE) which is also recommended by ENCODE guideline.

Hope to hear more comments and suggestions.

Many thanks,




On Fri, Apr 12, 2013 at 3:50 AM, Moritz Hess <ssehztirom@googlemail.com>wrote:

> 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@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@garvan.org.au
>> >wrote:
>>
>> > It is a question to ask at Biostars which has the address
>> > http://www.biostars.org/
>>
>>
>>
>> <zhangxl@bu.edu>
>>
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>
>
>
> --
>
> *Moritz Heß
> PhD Candidate
> *
> *Research associate
> Forest Research Institute
> of Baden Württemberg (FVA)
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> 79100 Freiburg (Germany)
>
> phone +49 761 4018 301*
>


<zhangxl@bu.edu>

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