Hi Luvina and all, for the builds in the main site, in enseGene table, after summation of all exon sizes in exonstarts,exonEnds (using zero-based start, and one-based end), we get exactly the total size of the transcript, as it appears in the relevant ensembl fasta file. Yet, for builds in the test site, with fragmented transcript sequences (occurence of large Ns blocks within the transcripts), the exon sizes do not sum up correctly. Generally, I would like to be able to exactly map the transcript to the genomic sequences, so how this could be done ? is there a way to do so despite the forgoing problem ?
Assaf On Fri, Jul 8, 2011 at 9:21 PM, Luvina Guruvadoo <[email protected]>wrote: > Hi Asaf, > > This is correct; the Ensembl gene track information corresponds to the > ensGene build in the Table Browser. > > Regards, > > --- > Luvina Guruvadoo > UCSC Genome Bioinformatics Group > > On 7/8/2011 11:00 AM, asas asasa wrote: > >> thanks luvina, >> >> just to make sure: >> Is the enseGene track information should also refer to the enseGene of >> corresponding build in the Table browser ? >> >> Thanks, >> Assaf >> >> On Fri, Jul 8, 2011 at 8:42 PM, Luvina Guruvadoo <[email protected]<mailto: >> [email protected]>> wrote: >> >> Hi Assaf, >> >> You can find this information by viewing the Ensembl track >> description page for each assembly. Using squirrel as an example, see >> http://genome-test.cse.ucsc.**edu/cgi-bin/hgTrackUi?&db=** >> speTri1&g=ensGene<http://genome-test.cse.ucsc.edu/cgi-bin/hgTrackUi?&db=speTri1&g=ensGene> >> <http://genome-test.cse.ucsc.**edu/cgi-bin/hgTrackUi?&db=** >> speTri1&g=ensGene<http://genome-test.cse.ucsc.edu/cgi-bin/hgTrackUi?&db=speTri1&g=ensGene> >> >. >> >> Please contact us again at [email protected] >> <mailto:[email protected]> if you have further questions. >> >> >> --- >> Luvina Guruvadoo >> UCSC Genome Bioinformatics Group >> >> >> >> On 7/8/2011 7:29 AM, asas asasa wrote: >> >> Hello all, >> >> I'm preparing a local mysql database with different UCSC >> tables, including >> ensGene/pep/gtp downloaded from the Table Browser. If I >> understand correctly >> these ensembl tables correspond to the last ensembl version >> published in the >> release notes here: >> >> http://genome.ucsc.edu/**goldenPath/releaseLog.html<http://genome.ucsc.edu/goldenPath/releaseLog.html>(it >> is >> now version 62 in most cases)... >> I also want to add those genomes that are absent in the >> formal site (e.g. >> Squirrel, Pika, Tree shrew, etc....), and found in >> http://genome-test.cse.ucsc.**edu<http://genome-test.cse.ucsc.edu>. >> Ensembl table for these >> genomes can be >> downloaded from the Table Browser in the test site: >> http://genome-test.cse.ucsc.**edu/<http://genome-test.cse.ucsc.edu/>, >> but which ensembl version do >> they >> correspond to ? >> >> Best wishes, >> Assaf >> ______________________________**_________________ >> Genome maillist - [email protected] >> <mailto:[email protected]> >> >> >> https://lists.soe.ucsc.edu/**mailman/listinfo/genome<https://lists.soe.ucsc.edu/mailman/listinfo/genome> >> >> >> >> > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
