Hi, I am getting an error message, when running the transcriptDB command from UCSC dm3KG <- makeTranscriptDbFromUCSC(genome="dm3", tablename="knownGene")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 I checked the tables supported by UCSC, The table is there: > supportedUCSCtables() track subtrack knownGene UCSC Genes <na> knownGeneOld3 Old UCSC Genes <na> wgEncodeGencodeManualV3 Gencode Genes Genecode Manual Doing the same with the ensembl table works perfectly fine. Does anyone has an Idea as to why this is happening? Thanks Assa [[alternative HTML version deleted]]

Hi Assa, On 11-07-28 07:58 AM, Assa Yeroslaviz wrote: > Hi, > > I am getting an error message, when running the transcriptDB command from > UCSC > > dm3KG<- makeTranscriptDbFromUCSC(genome="dm3", > tablename="knownGene")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 > > I checked the tables supported by UCSC, The table is there: > >> supportedUCSCtables() track subtrack > knownGene UCSC Genes<na> > knownGeneOld3 Old UCSC Genes<na> > wgEncodeGencodeManualV3 Gencode Genes Genecode Manual Not all the supported tables/tracks are available for all organisms. UCSC only provides the "UCSC Genes" track for Human, Rat and Mouse. For Fly you can either use the refGene table ("RefSeq Genes" track) or the enGene table ("Ensembl Genes" track). See here for all the tracks available for Fly at UCSC: http://genome.ucsc.edu/cgi-bin/hgTracks?clade=insect&org=D.+melanogast er&db=dm3&position=chr2L%3A826%2C001-851%2C000&hgt.suggest=&hgt.sugges tTrack=refGene&pix=800&Submit=submit&hgsid=204682653 > > > Doing the same with the ensembl table works perfectly fine. With makeTranscriptDbFromBiomart() you get the Ensembl genes, not the UCSC genes. Cheers, H. > > Does anyone has an Idea as to why this is happening? > > Thanks > Assa > > [[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