Re: [Transdecoder-users] output files
Extracting likely coding regions from transcript sequences
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bhaas
From: Brian H. <bh...@br...> - 2014-08-20 11:42:28
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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 The documentation could be out of date.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 Is the documentation (http://transdecoder.sourceforge.net/) out of date, or is the transdecoder failing silently, I couldnt see any issues with memory usage etc.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 > |