Re: [Transdecoder-users] output files

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

Thanks for the update! Glad to hear it's working 

Best,

-Brian
(by iPhone)


> On Aug 20, 2014, at 5:29 AM, Jon Lees <jon...@gm...> wrote:
> 
> Hi Brian
> 
> Actually,  apologies, it looks like Transdecoder is working fine,
> a trans spliced gene had caused some problems in the transcriptome build,
> generating a very large erroneous transcript sequence,,
> 
> Thanks and best wishes
> 
> Jon
> 
> 
> 
> 
> 
>> On Tue, Aug 19, 2014 at 12:48 PM, Brian Haas <bh...@br...> wrote:
>> OK - I look forward to learning more.  
>> 
>> thx,
>> 
>> ~brian
>> 
>> 
>> 
>>> On Tue, Aug 19, 2014 at 7:45 AM, Jon Lees <jon...@gm...> wrote:
>>> 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 The documentation could be out of date.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 Is the documentation (http://transdecoder.sourceforge.net/) out of date, or is the transdecoder failing silently, I couldnt see any issues with memory usage etc.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
>> 
>> 
>> 
>> -- 
>> --
>> Brian J. Haas
>> The Broad Institute
>> http://broad.mit.edu/~bhaas
>