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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> _______________________________________________
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> Tra...@li...
> https://lists.sourceforge.net/lists/listinfo/transdecoder-users
>
>
--
--
Brian J. Haas
The Broad Institute
http://broad.mit.edu/~bhaas
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