Re: [Transdecoder-users] Transdecoder via Trinity Not Outputting final files

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

Hi Summer,

It's likely that you're working from an older Trinity installation.  If so,
you can find the corresponding documentation in the $TRINITY_HOME/docs
folder.

It's best, though, to upgrade to a newer version. We try to keep the web
documentation consistent with whatever the latest production Trinity
release is.

best,

~brian



On Wed, Mar 19, 2014 at 6:19 PM, Elasady, Summer <sr...@st...> wrote:

>   Hello-
>
>  I'm trying to run Transdecoder from within Trinity, and the instructions
> say to run:
>
>  $TRINITY_HOME/trinity-plugins/transdecoder/TransDecoder
>
>
> However, I don't have that option in my file path. In the /transdecoder/ folder I have two perl scripts titled:
>
>
>    -
>
>    transcripts_to_best_scoring_ORFs.pl
>    -
>
>    cdna_alignment_orf_to_genome_orf.pl
>
>
> The cdna_alignment script does not work, and when I run the transcripts to
> best scoring ORFs, it does not output the final files needed for downstream
> analysis, but it does output the preliminary files. I'm using Trinity from
> 02.25.2013.
>
>  Any ideas on what to do?
>
>  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