Re: [Transdecoder-users] File for Training

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

Alexie - can you respond to this?  It's one of the options you incorporated.

thanks,

~brian


On Fri, May 2, 2014 at 5:37 AM, 卢 汉斌 <lh...@gm...> wrote:

> Hello,
>
> I try to find coding regions within transcripts using TransDecoder.  I
> want to use the close species (with relatively detailed genome annotation)
> to train Markov Mod for protein identification. I don’t quite understand
> what kind of file should I transmit to “—train” option, whether the
> annotation protein FASTA file or annotation CDS FASTA file of the close
> species?
>
> Also, the annotation proteins of this close species still contain a
> portion of low confidence genes. Should I filter out those low confidence
> genes or pick up some high confidence ORFs for training Markov Mod?
>
> Thank you for you advise.
>
> Best,
> David
>
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Brian J. Haas
The Broad Institute
http://broad.mit.edu/~bhaas