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

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

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...