how to make transcript db from ucsc for mm8
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Ou, Jianhong ★ 1.3k
@ou-jianhong-4539
Last seen 19 hours ago
United States
Hi, I got error when I make transcript db from ucsc for mm8. Could anybody help me to figure out this? Thanks in advance. Error in tableNames(ucscTableQuery(session, track = track)) : error in evaluating the argument 'object' in selecting a method for function 'tableNames': Error in normArgTrack(track, trackids) : Unknown track: UCSC Genes The codes: Library(GenomicFeatures) mm8KG <- makeTranscriptDbFromUCSC(genome="mm8", tablename="knownGene") sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] GenomicFeatures_1.14.0 AnnotationDbi_1.24.0 Biobase_2.22.0 rtracklayer_1.22.0 GenomicRanges_1.14.3 XVector_0.2.0 IRanges_1.20.5 [8] BiocGenerics_0.8.0 loaded via a namespace (and not attached): [1] biomaRt_2.18.0 Biostrings_2.30.0 bitops_1.0-6 BSgenome_1.30.0 DBI_0.2-7 RCurl_1.95-4.1 Rsamtools_1.14.1 RSQLite_0.11.4 stats4_3.0.2 [10] tools_3.0.2 XML_3.95-0.2 zlibbioc_1.8.0 Yours sincerely, Jianhong Ou LRB 670A Program in Gene Function and Expression 364 Plantation Street Worcester, MA 01605 [[alternative HTML version deleted]]
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@herve-pages-1542
Last seen 15 hours ago
Seattle, WA, United States
Hi Jianhong, Thanks for the report. Problem came from the fact that makeTranscriptDbFromUCSC() was assuming that the "knownGene" table was always associated with the "UCSC Genes" track but this appears to not be true for old Human/Mouse/Rat assemblies where the track is called "Known Genes". This is fixed in GenomicFeatures 1.14.1 (release) and 1.15.3 (devel). Both should become available via biocLite() in the next 30 hours or so. Cheers, H. On 11/13/2013 01:46 PM, Ou, Jianhong wrote: > Hi, > > I got error when I make transcript db from ucsc for mm8. Could anybody help me to figure out this? Thanks in advance. > > Error in tableNames(ucscTableQuery(session, track = track)) : > error in evaluating the argument 'object' in selecting a method for function 'tableNames': Error in normArgTrack(track, trackids) : Unknown track: UCSC Genes > > The codes: > Library(GenomicFeatures) > mm8KG <- makeTranscriptDbFromUCSC(genome="mm8", tablename="knownGene") > > sessionInfo() > R version 3.0.2 (2013-09-25) > Platform: x86_64-apple-darwin10.8.0 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods base > > other attached packages: > [1] GenomicFeatures_1.14.0 AnnotationDbi_1.24.0 Biobase_2.22.0 rtracklayer_1.22.0 GenomicRanges_1.14.3 XVector_0.2.0 IRanges_1.20.5 > [8] BiocGenerics_0.8.0 > > loaded via a namespace (and not attached): > [1] biomaRt_2.18.0 Biostrings_2.30.0 bitops_1.0-6 BSgenome_1.30.0 DBI_0.2-7 RCurl_1.95-4.1 Rsamtools_1.14.1 RSQLite_0.11.4 stats4_3.0.2 > [10] tools_3.0.2 XML_3.95-0.2 zlibbioc_1.8.0 > > Yours sincerely, > > Jianhong Ou > > LRB 670A > Program in Gene Function and Expression > 364 Plantation Street Worcester, > MA 01605 > > [[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 > -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319
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Dear Herve, Great. Thanks a lot for your work. Yours sincerely, Jianhong Ou LRB 670A Program in Gene Function and Expression 364 Plantation Street Worcester, MA 01605 On 11/16/13 6:51 AM, "Hervé Pagès" <hpages at="" fhcrc.org=""> wrote: >Hi Jianhong, > >Thanks for the report. Problem came from the fact that >makeTranscriptDbFromUCSC() was assuming that the "knownGene" table >was always associated with the "UCSC Genes" track but this appears to >not be true for old Human/Mouse/Rat assemblies where the track is >called "Known Genes". > >This is fixed in GenomicFeatures 1.14.1 (release) and 1.15.3 >(devel). Both should become available via biocLite() in the >next 30 hours or so. > >Cheers, >H. > > >On 11/13/2013 01:46 PM, Ou, Jianhong wrote: >> Hi, >> >> I got error when I make transcript db from ucsc for mm8. Could anybody >>help me to figure out this? Thanks in advance. >> >> Error in tableNames(ucscTableQuery(session, track = track)) : >> error in evaluating the argument 'object' in selecting a method for >>function 'tableNames': Error in normArgTrack(track, trackids) : Unknown >>track: UCSC Genes >> >> The codes: >> Library(GenomicFeatures) >> mm8KG <- makeTranscriptDbFromUCSC(genome="mm8", tablename="knownGene") >> >> sessionInfo() >> R version 3.0.2 (2013-09-25) >> Platform: x86_64-apple-darwin10.8.0 (64-bit) >> >> locale: >> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >> >> attached base packages: >> [1] parallel stats graphics grDevices utils datasets methods >> base >> >> other attached packages: >> [1] GenomicFeatures_1.14.0 AnnotationDbi_1.24.0 Biobase_2.22.0 >> rtracklayer_1.22.0 GenomicRanges_1.14.3 XVector_0.2.0 >>IRanges_1.20.5 >> [8] BiocGenerics_0.8.0 >> >> loaded via a namespace (and not attached): >> [1] biomaRt_2.18.0 Biostrings_2.30.0 bitops_1.0-6 >>BSgenome_1.30.0 DBI_0.2-7 RCurl_1.95-4.1 Rsamtools_1.14.1 >>RSQLite_0.11.4 stats4_3.0.2 >> [10] tools_3.0.2 XML_3.95-0.2 zlibbioc_1.8.0 >> >> Yours sincerely, >> >> Jianhong Ou >> >> LRB 670A >> Program in Gene Function and Expression >> 364 Plantation Street Worcester, >> MA 01605 >> >> [[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 >> > >-- >Hervé Pagès > >Program in Computational Biology >Division of Public Health Sciences >Fred Hutchinson Cancer Research Center >1100 Fairview Ave. N, M1-B514 >P.O. Box 19024 >Seattle, WA 98109-1024 > >E-mail: hpages at fhcrc.org >Phone: (206) 667-5791 >Fax: (206) 667-1319
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