Re: [Transdecoder-users] output files

[Jon L. <jon...@gm...>]

Hi Brian
Yes I just tried that, and it looks like the documentation is up to date,
but its silently crashing at some point.

Ive just started trying to debug to find out at which point its stops
running
will let you know if I find anything

thanks and
best wishes

Jon




On Tue, Aug 19, 2014 at 12:35 PM, Brian Haas <bh...@br...>
wrote:

> 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 The documentation could be out of date.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 Is the documentation (http://transdecoder.sourceforge.net/) out of date,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
>
>
>