Hello Valeria, The track 'Known Genes" has been replaced with track called "UCSC Genes". The data generation rules are a bit different. But the methods from the link sent you should work with pulling out transcripts by Gene ID.
The track called "Old UCSC Genes" is the process used for the prior track "Known Genes" in the link sent to you. Compare the track details (methods, etc) for each to understand a bit about the processing differences. The idea behind each version is to create a composite of all high quality known transcripts that create distinct translated proteins and pool them together into non-redundant group group by gene bound. This is of course a work-in-progress as the genome moves closer towards basic annotation completion (all core gene locations and variants & transcripts identified). Hope this helps, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Valeria Vasta" <[email protected]> wrote: > From: "Valeria Vasta" <[email protected]> > To: "Katrina Learned" <[email protected]>, [email protected] > Sent: Monday, September 7, 2009 2:53:46 PM GMT -08:00 US/Canada Pacific > Subject: Re: [Genome] search genes with GeneID > > Hello > > I have to use Entrez Gene IDs in order to get the exon coordinates > for > many genes. I want to use the gene ID rather than the name to get to > the > ucs genes and then the exon coordinates > > I looked at the link below and tried the Table browser. However at > Track > there's no Known Genes option; if I chose refSeq genes then at table > there's no knowntolocuslink option > > > Please let me know > > Thanks a lot > > Valeria Vasta > -----Original Message----- > From: Katrina Learned [mailto:[email protected]] > Sent: Thursday, July 09, 2009 1:07 PM > To: Vasta, Valeria > Subject: Re: [Genome] search genes with GeneID > > Hi Valeria, > > I am sorry that I misunderstood your question. > > Yes, this is possible. Please see this previous mailing list answer > for > directions on exactly how to do this with our Table Browser (click on > > "Tables" in the blue menu bar at the top of the page): > https://lists.soe.ucsc.edu/pipermail/genome/2006-November/012212.html > > In the future, please direct your questions to the genome mailing list > > at [email protected]. You will likely get a quicker response to your > > question. > > Katrina Learned > UCSC Genome Bioinformatics Group > > > > Vasta, Valeria wrote: > > The thing is that I need to search a long list of genes, so far I > could > > do it only with the name TABLE-KNOWN GENE_PASTE LIST > > Any way to do it with the #? > > > > Valeria > > > > -----Original Message----- > > From: Katrina Learned [mailto:[email protected]] > > Sent: Wednesday, July 08, 2009 8:00 AM > > To: Vasta, Valeria > > Cc: [email protected] > > Subject: Re: [Genome] search genes with GeneID > > > > Dear Valeria, > > > > You can search for genes using the geneID# from NCBI gene page > (Entrez > > > Gene). To do so, type the gene ID in the "position/search" field of > the > > Genome Browser. > > > > Please don't hesitate to contact the mail list if you require > further > > assistance. > > > > Katrina Learned > > UCSC Genome Bioinformatics Group > > > > > > > > Vasta, Valeria wrote: > > > >> Hello > >> > >> > >> > >> Is it possible to search genes using geneID# from NCBI Gene page > >> instead of gene names? I noticed that gene names can pull out > genes > >> > > that > > > >> are not related but have the same name by chance > >> > >> thanks > >> > >> > >> > >> Valeria > >> > >> > >> > >> Children's Hospital and Regional Medical Center is now Seattle > >> > > Children's. > > > >> CONFIDENTIALITY NOTICE: This e-mail message, including any > >> > > attachments, is for the sole use of the intended recipient(s) and > may > > contain confidential and privileged information protected by law. > Any > > unauthorized review, use, disclosure or distribution is prohibited. > If > > you are not the intended recipient, please contact the sender by > reply > > e-mail and destroy all copies of the original message. > > > >> _______________________________________________ > >> Genome maillist - [email protected] > >> https://lists.soe.ucsc.edu/mailman/listinfo/genome > >> > >> > > > > Children's Hospital and Regional Medical Center is now Seattle > Children's. > > CONFIDENTIALITY NOTICE: This e-mail message, including any > attachments, is for the sole use of the intended recipient(s) and may > contain confidential and privileged information protected by law. > Any > unauthorized review, use, disclosure or distribution is prohibited. > If > you are not the intended recipient, please contact the sender by > reply > e-mail and destroy all copies of the original message. > > > > > > CONFIDENTIALITY NOTICE: This e-mail message, including any > attachments, is for the sole use of the intended recipient(s) and may > contain confidential and privileged information protected by law. Any > unauthorized review, use, disclosure or distribution is prohibited. > If you are not the intended recipient, please contact the sender by > reply e-mail and destroy all copies of the original message. > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
