Dear List, I am creating a TranscriptDatabase as follows: library(GenomicFeatures) myDB <- makeTranscriptDbFromBiomart(biomart = "ensembl", dataset = "scerevisiae_gene_ensembl", circ_seqs = c(DEFAULT_CIRC_SEQS, "Mito")) myDBx <- cdsBy(myDB, by = "tx", use.names = TRUE) everything fine so far, I am just missing 4 ORFs which are present on the 2 micron plasmid. (R0010W, R0020C, R0030W, R0040C) If one puts here http://www.yeastgenome.org/cgi-bin/seqTools "R0010W", one finds the following info: FLP1/R0010W, ORF, on 2-micron plasmid from coordinates 252 to 1523. While the annotation from Ensembl is imported from SGD, no ORFs are listed for the 2-micron plasmid, and therefore also not accessible via makeTranscriptDbFromBiomart. Any hints what I am getting wrong? Best, Stefanie [[alternative HTML version deleted]]

Hi Stefanie, Not a good idea to start a new thread by replying to an old one. This confuses most thread-aware email client as they will place the new question deep inside the old thread, and as a result most people won't see it. On 03/05/2013 01:34 AM, Stefanie Tauber wrote: > Dear List, > > I am creating a TranscriptDatabase as follows: > > library(GenomicFeatures) > myDB <- makeTranscriptDbFromBiomart(biomart = "ensembl", dataset = "scerevisiae_gene_ensembl", circ_seqs = c(DEFAULT_CIRC_SEQS, "Mito")) > myDBx <- cdsBy(myDB, by = "tx", use.names = TRUE) > > everything fine so far, > I am just missing 4 ORFs which are present on the 2 micron plasmid. (R0010W, R0020C, R0030W, R0040C) There doesn't seem to be any 2-micron plasmid in the Yeast reference genome currently in use by Ensembl: > seqlengths(myDB) I II III IV V VI VII VIII IX X 230218 813184 316620 1531933 576874 270161 1090940 562643 439888 745751 XI XII XIII XIV XV XVI Mito 666816 1078177 924431 784333 1091291 948066 85779 No 2-micron plasmid either in UCSC sacCer3: > library(BSgenome.Scerevisiae.UCSC.sacCer3) > Scerevisiae Yeast genome | | organism: Saccharomyces cerevisiae (Yeast) | provider: UCSC | provider version: sacCer3 | release date: April 2011 | release name: SGD April 2011 sequence | | sequences (see '?seqnames'): | chrI chrII chrIII chrIV chrV chrVI chrVII chrVIII | chrIX chrX chrXI chrXII chrXIII chrXIV chrXV chrXVI | chrM | | (use the '$' or '[[' operator to access a given sequence) > seqlengths(Scerevisiae) chrI chrII chrIII chrIV chrV chrVI chrVII chrVIII chrIX chrX 230218 813184 316620 1531933 576874 270161 1090940 562643 439888 745751 chrXI chrXII chrXIII chrXIV chrXV chrXVI chrM 666816 1078177 924431 784333 1091291 948066 85779 The 2 Yeast genomes above (Ensembl and UCSC) seem to be the same even though having the same chromosome lengths is not a guarantee that the sequences are actually the same. > > > If one puts here http://www.yeastgenome.org/cgi-bin/seqTools "R0010W", > one finds the following info: > FLP1/R0010W, ORF, on 2-micron plasmid from coordinates 252 to 1523. > > > While the annotation from Ensembl is imported from SGD, no ORFs are listed for the 2-micron plasmid, and therefore > also not accessible via makeTranscriptDbFromBiomart. > > Any hints what I am getting wrong? I'm not sure why the 2-micron plasmid was dropped by Ensembl (and UCSC) but that sounds more like a question for them. H. > > Best, > Stefanie > [[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