Hello Oliver, For the Ensembl Genes track, associated tables can be viewed together in the Table browser, making it easier to review the complete dataset. Bring up the assembly and track, and use the "describe table schema" button next to the default table (ensGene).
http://genome.ucsc.edu/cgi-bin/hgTables ensGene has the transcript name in the field "name" (the description is misleading as it states this is a gene, a legacy naming issue, please ignore). ensGene links to ensGtp (ensGtp.transcript <-> ensGene.name). In ensGtp, there are three identifiers: gene (ENSG...), transcript (ENST...), and protein (ENSP...). For the genome data in ucscToEnsembl, again, it is very possible that Ensembl has a additional genome data generated/incorporated since the initial release of GRCh37 at NCBI. UCSC's version of GRCh37 is NCBI Build 37.1. There are no plans to update the core genome assembly for GRCh37 at this time. Hopefully this helps to explain the data, Jennifer --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 6/2/10 3:10 AM, Oliver Lui wrote: > > Hi there > > I tried to download the ensGene table in the GRCh37/ hg19 database in GTF > format, but the gene ids and the transcript ids are always the same, i.e. > start with "ENST". I think the gene ids should start with "ENSG"? > > Also, I've downloaded the latest human GTF file (Homo_sapiens.GRCh37.58.gtf) > from the Ensembl website, but I couldn't find the corresponding ucsc ids for > some of the Ensembl ids (at the bottom of the file), e.g. LRG_15, from the > ucscToEnsembl table. Any suggestion about what I could do? > > Thanks! > > Regards > Oliver > > _________________________________________________________________ > http://clk.atdmt.com/UKM/go/197222280/direct/01/ > Do you have a story that started on Hotmail? Tell us now > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
