I was following Mike's RNAseq workflow from here http://www.bioconductor.org/help/workflows/rnaseqGene/
and it had exon_name's - but that's probably because the txdb is made from NCBI (GrCh37.75) Thanks for the clarification Herve and Marc! Sonali. On 9/22/2015 5:39 PM, Marc Carlson wrote: > Herve is right. UCSC doesn't give us this information, And actually, > I think it's pretty rare to see exon names from anybody. So it's > weird to me that they are a default return value for this method. > > Marc > > On Tue, Sep 22, 2015 at 5:29 PM, Hervé Pagès <hpa...@fredhutch.org > <mailto:hpa...@fredhutch.org>> wrote: > > Hi Sonali, > > UCSC doesn't provide names for the exons of their gene models. > See the table where this data is coming from: > > > > https://genome.ucsc.edu/cgi-bin/hgTables?db=hg19&hgta_group=genes&hgta_track=knownGene&hgta_table=knownGene&hgta_doSchema=describe+table+schema > > The exon information is all coming from the exonStarts and exonEnds > columns. No exon names! > > H. > > PS: Maybe this would better be asked on the support site. > > > On 09/22/2015 04:44 PM, Arora, Sonali wrote: > > Hi everyone, > > I was trying to get the exons by gene from a txdb object but I > get NA's > for all exon_name's. Please advise. > > > library(TxDb.Hsapiens.UCSC.hg19.knownGene) > > txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene > > ebg2 <- exonsBy(txdb, by="gene") > > > > ebg2 > GRangesList object of length 23459: > $1 > GRanges object with 15 ranges and 2 metadata columns: > seqnames ranges strand | exon_id > <Rle> <IRanges> <Rle> | <integer> > [1] chr19 [58858172, 58858395] - | 250809 > [2] chr19 [58858719, 58859006] - | 250810 > [3] chr19 [58859832, 58860494] - | 250811 > [4] chr19 [58860934, 58862017] - | 250812 > [5] chr19 [58861736, 58862017] - | 250813 > ... ... ... ... ... ... > [11] chr19 [58868951, 58869015] - | 250821 > [12] chr19 [58869318, 58869652] - | 250822 > [13] chr19 [58869855, 58869951] - | 250823 > [14] chr19 [58870563, 58870689] - | 250824 > [15] chr19 [58874043, 58874214] - | 250825 > exon_name > <character> > [1] <NA> > [2] <NA> > [3] <NA> > [4] <NA> > [5] <NA> > ... ... > [11] <NA> > [12] <NA> > [13] <NA> > [14] <NA> > [15] <NA> > > $10 > GRanges object with 2 ranges and 2 metadata columns: > seqnames ranges strand | exon_id exon_name > [1] chr8 [18248755, 18248855] + | 113603 <NA> > [2] chr8 [18257508, 18258723] + | 113604 <NA> > > ... > <23457 more elements> > ------- > seqinfo: 93 sequences (1 circular) from hg19 genome > > testgr <- unlist(ebg2) > > table(is.na <http://is.na>(mcols(testgr)$exon_name)) > > TRUE > 272776 > > sessionInfo() > R version 3.2.2 RC (2015-08-09 r68965) > Platform: x86_64-w64-mingw32/x64 (64-bit) > Running under: Windows 7 x64 (build 7601) Service Pack 1 > > locale: > [1] LC_COLLATE=English_United States.1252 > [2] LC_CTYPE=English_United States.1252 > [3] LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] stats4 parallel stats graphics grDevices utils > [7] datasets methods base > > other attached packages: > [1] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.1 > [2] GenomicFeatures_1.21.29 > [3] AnnotationDbi_1.31.18 > [4] Biobase_2.29.1 > [5] GenomicRanges_1.21.28 > [6] GenomeInfoDb_1.5.16 > [7] IRanges_2.3.21 > [8] S4Vectors_0.7.18 > [9] BiocGenerics_0.15.6 > > loaded via a namespace (and not attached): > [1] XVector_0.9.4 zlibbioc_1.15.0 > [3] GenomicAlignments_1.5.17 BiocParallel_1.3.52 > [5] tools_3.2.2 SummarizedExperiment_0.3.9 > [7] DBI_0.3.1 lambda.r_1.1.7 > [9] futile.logger_1.4.1 rtracklayer_1.29.27 > [11] futile.options_1.0.0 bitops_1.0-6 > [13] RCurl_1.95-4.7 biomaRt_2.25.3 > [15] RSQLite_1.0.0 Biostrings_2.37.8 > [17] Rsamtools_1.21.17 XML_3.98-1.3 > > > -- > 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: hpa...@fredhutch.org <mailto:hpa...@fredhutch.org> > Phone: (206) 667-5791 <tel:%28206%29%20667-5791> > Fax: (206) 667-1319 <tel:%28206%29%20667-1319> > > > _______________________________________________ > Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> mailing > list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > -- Thanks and Regards, Sonali Office: C2-169 http://tinyurl.com/sonali-hb-calendar [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
