I would recommend calling gr <- import(gff) And then subset for the type being exon and tabulate by parent. Michael On Thu, Sep 4, 2014 at 8:14 AM, Jon Br?te <jon.brate at="" ibv.uio.no=""> wrote: > Thanks Michael, > > Yes you are right. Many of the transcripts come from multiple > chromosomes (or scaffolds because this is a poorly assembled genome and > that is probably why there is so much trans-splicing). > > I think removing the trans-spliced genes removes too many genes so I > will try to do this in another way. > > Thank you, > > Jon > > > On 4. sep. 2014, at 13:56, Michael Lawrence wrote: > > I think the error messages are a pretty good clue to what's wrong here. > The TxDb needs to know the "rank" (the order within the transcript) of each > exon. It tries to infer this from the positions, but this obviously fails > when exons within the same transcript fall on multiple chromosomes > (trans-splicing). When parsing the GTF, there is some problem with the > format. You could figure out the offending line(s) by cutting the file in > half recursively until the error goes away. > > If you want, you could put the files up on dropbox, and I'll take a look > at them. > > Michael > > > > On Thu, Sep 4, 2014 at 3:23 AM, Jon Br?te <jon.brate at="" ibv.uio.no=""> wrote: > >> Hi list, >> >> I am trying to create a TranscriptDb using GenomicFeatures, but I get an >> error message. I think there might be something wrong with my gff- file, but >> I am not sure. I also tried converting the gff-file to gtf, but also get an >> error. >> >> My goal with this is to plot the number of exons per gene. >> >> Code: >> >> #GFF-file >> > txdb = makeTranscriptDbFromGFF(file = >> "~/Documents/Prosjekter/RNA-project/Data/Sycon_ciliatum/sycon-from- Bergen/gff-files-and-expression-levels/cds.gb.gff3", >> + format = "gff") >> extracting transcript information >> Extracting gene IDs >> extracting transcript information >> Processing splicing information for gff3 file. >> Deducing exon rank from relative coordinates provided >> Warning message: >> In .deduceExonRankings(exs, format = "gff") : >> Infering Exon Rankings. If this is not what you expected, then please >> be sure that you have provided a valid attribute for exonRankAttributeName >> Error in unlist(mapply(.assignRankings, starts, strands)) : >> error in evaluating the argument 'x' in selecting a method for function >> 'unlist': Error in (function (starts, strands) : >> Exon rank inference cannot accomodate trans-splicing. >> >> #GTF-file >> > txdbGTF = makeTranscriptDbFromGFF(file = >> "~/Documents/Prosjekter/RNA-project/Data/Sycon_ciliatum/sycon-from- Bergen/gff-files-and-expression-levels/cds.gb.gtf", >> + format = "gtf") >> Error in .parse_attrCol(attrCol, file, colnames) : >> Some attributes do not conform to 'tag value' format >> >> >> > sessionInfo() >> R version 3.1.0 (2014-04-10) >> Platform: x86_64-apple-darwin10.8.0 (64-bit) >> >> locale: >> [1] C >> >> attached base packages: >> [1] parallel stats graphics grDevices utils datasets methods >> base >> >> other attached packages: >> [1] GenomicFeatures_1.16.2 AnnotationDbi_1.26.0 Biobase_2.24.0 >> GenomicRanges_1.16.3 >> [5] GenomeInfoDb_1.0.2 IRanges_1.22.10 BiocGenerics_0.10.0 >> >> loaded via a namespace (and not attached): >> [1] BBmisc_1.7 BSgenome_1.32.0 BatchJobs_1.3 >> BiocParallel_0.6.1 >> [5] Biostrings_2.32.1 DBI_0.2-7 >> GenomicAlignments_1.0.5 RCurl_1.95-4.3 >> [9] RSQLite_0.11.4 Rcpp_0.11.2 Rsamtools_1.16.1 >> XML_3.98-1.1 >> [13] XVector_0.4.0 biomaRt_2.20.0 bitops_1.0-6 >> brew_1.0-6 >> [17] checkmate_1.3 codetools_0.2-9 digest_0.6.4 >> fail_1.2 >> [21] foreach_1.4.2 iterators_1.0.7 rtracklayer_1.24.2 >> sendmailR_1.1-2 >> [25] stats4_3.1.0 stringr_0.6.2 tools_3.1.0 >> zlibbioc_1.10.0 >> >> >> ---------------------------------------------------------------- >> Jon Br?te >> >> Section for Genetics and Evolutionary Biology (EVOGENE) >> Department of Biosciences >> University of Oslo >> P.B. 1066 Blindern >> N-0316, Norway >> Email: jon.brate at ibv.uio.no<mailto:jon.brate at="" ibv.uio.no=""> >> Phone: 922 44 582 >> Web: mn.uio.no/ibv/english/people/aca/jonbra/index.html< >> http://mn.uio.no/ibv/english/people/aca/jonbra/index.html> >> >> >> >> >> >> [[alternative HTML version deleted]] >> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > > > > ---------------------------------------------------------------- > Jon Br?te > > Section for Genetics and Evolutionary Biology (EVOGENE) > Department of Biosciences > University of Oslo > P.B. 1066 Blindern > N-0316, Norway > Email: jon.brate at ibv.uio.no > Phone: 922 44 582 > Web: mn.uio.no/ibv/english/people/aca/jonbra/index.html > > > > > [[alternative HTML version deleted]]