transdecoder-users

[Transdecoder-users] Extract only best ORF

[Elasady, S. <sr...@st...>]

Hello-

Is there a way to have transdecoder output only a single “best” ORF?

Thank you,

Summer R. Elasady
Baumann Lab - Bioinformatics Intern
SR...@st...

Re: [Transdecoder-users] Extract only best ORF

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

Hi Summer,

This has been a popular request.  It doesn't do it now, but we could
consider it for a future release.

best,

~brian


On Mon, Apr 14, 2014 at 10:49 AM, Elasady, Summer <sr...@st...> wrote:

>   Hello-
>
>  Is there a way to have transdecoder output only a single “best” ORF?
>
>  Thank you,
>
>  Summer R. Elasady
> Baumann Lab - Bioinformatics Intern
> SR...@st...
>
>
>
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>


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

Re: [Transdecoder-users] Extract only best ORF

[<Ale...@cs...>]

Some Qs as it is not clear in my head:

  *   You mean a single ORF per Trinity sequence ?
  *   What is it affecting if you have two ORFs?
  *   What would be the metric that would score this (and makes biological sense)?
  *   How would you deal with Trinity sequences that have two real ORFs?

a

________________________________
From: Elasady, Summer [sr...@st...]
Sent: Tuesday, 15 April 2014 12:49 AM
To: tra...@li...
Subject: [Transdecoder-users] Extract only best ORF

Hello-

Is there a way to have transdecoder output only a single “best” ORF?

Thank you,

Summer R. Elasady
Baumann Lab - Bioinformatics Intern
SR...@st...