Re: [Transdecoder-users] TransDecoder

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

Hi Suhaila,

I don't think there's a hard limit for what you can select as a parameter
value, but note the false discovery rate is bound to go up exponentially as
you start lowering the min length.

best,

~brian

On Thu, Oct 2, 2014 at 10:27 AM, Suhaila Sulaiman <
suh...@gm...> wrote:

> 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
>>
>>
>>
>
>


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