Re: [Transdecoder-users] TransDecoder

[Suhaila S. <suh...@gm...>]

Hi Brian,

Thanks for your prompt reply. Really helpful.

One more question here. In TransDecode, default length of ORFs predicted is
100 amino acids (-m parameter right?). Is there any minimum number of
length that the software can accept? In some cases, I need to search for
small ORF which is less than 80 residues. Can it goes until 10 residues or
20 residues?

Regards,

Suhaila.

On Wed, Oct 1, 2014 at 6:04 PM, Brian Haas <bh...@br...> wrote:

> 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
>
>
>