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: Jon L. <jon...@gm...> - 2014-08-20 09:29:40
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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 The documentation could be out of date.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 > > > |
