Re: [Transdecoder-users] output files
Extracting likely coding regions from transcript sequences
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Re: [Transdecoder-users] output files
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From: Brian H. <bh...@br...> - 2014-08-19 11:48:44
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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 The documentation could be out of date.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 |
