Thread: [Transdecoder-users] output files
Extracting likely coding regions from transcript sequences
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From: Jon L. <jon...@gm...> - 2014-08-19 10:27:54
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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directory e.g. """transcripts.fasta.transdecoder.pep""" Is the documentation (http://transdecoder.sourceforge.net/) out of date, or is the transdecoder failing silently, I couldnt see any issues with memory usage etc.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 |
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From: Brian H. <bh...@br...> - 2014-08-19 11:35:42
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HI Jon, The documentation could be out of date.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 Is the documentation (http://transdecoder.sourceforge.net/) out of date, 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 |
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From: Jon L. <jon...@gm...> - 2014-08-19 11:45:49
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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 > > > |
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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 |
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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 > > > |
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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 > |
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