Re: [Transdecoder-users] output files

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

HI Jon,

The documentation could be out of date.  Can you try running the sample
data set through and see if it generates the expected output files?

  cd sample_data/
   ./runMe.sh

best,

~brian




On Tue, Aug 19, 2014 at 6:27 AM, Jon Lees <jon...@gm...> wrote:

> Hi
>
> Ive run transdecoder a couple of times now,
>
> However it only generates the temporary folder
>
> with the three files:
> longest_orfs.pep   : all ORFs meeting the minimum length criteria,
> regardless of coding potential.
> longest_orfs.gff3  : positions of all ORFs as found in the target
> transcripts
> longest_orfs.cds   : the nucleotide coding sequence for all detected ORFs
>
> no other files are generated, e.g.:
>
> """longest_orfs.cds.top_500_longest"""
>
>
> or the final outputs files in the current working directory
>
>
> e.g. """transcripts.fasta.transdecoder.pep"""
>
>
> Is the documentation (http://transdecoder.sourceforge.net/) out of date,
> or is the transdecoder failing silently, I couldnt see any issues with
> memory usage etc.
>
> Thanks
>
>
> Jon
>



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