Re: [Transdecoder-users] TransDecoder

[Brian H. <bh...@br...>]

Hi Suhaila,

responses below:

On Tue, Sep 30, 2014 at 11:09 PM, Suhaila Sulaiman <
suh...@gm...> wrote:

> Hi,
>
> I am Suhaila, a PhD student from Malaysia. I am writing this email to ask
> something regarding TransDecoder program. Sorry as I just found the
> program, so the questions would be very basic though.
>
>    1. Let say I have RNA-seq data, I have assembled using Tophat and
>    Cufflinks, so I can directly use TransDecoder to predict for genes in the
>    assembled transcripts, right? Then using the result from TransDecoder, I
>    can mapped back the predicted genes against the annotated genes in the ref
>    genome, am I right?
>
> Yes, transdecoder will predict coding regions within the cufflinks-defined
transcripts.  This is described in the web documentation at
http://transdecoder.sf.net



>
>    1.
>    2. Is there any publication of TransDecoder that I can cited in my
>    research?
>
>
>
It's best to cite the website, but you can also cite:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3875132/
where the algorithm is described in the supp. materials.

best,

~brian


> Looking forward for your reply, and much appreciated!
>
> Regards,
> Suhaila S.
>



-- 
--
Brian J. Haas
The Broad Institute
http://broad.mit.edu/~bhaas