Hi Shobha, Unfortunately, there isn't a way to use the table browser to put the gene symbols from the kgXref table in GTF format. You will need to write a script to do this for you.
If you have further questions, please contact the mailing list: [email protected]. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ----- Original Message ----- From: "Shobha Potluri" <[email protected]> To: "Antonio Coelho" <[email protected]> Cc: [email protected] Sent: Thursday, May 12, 2011 1:44:50 PM Subject: Re: [Genome] Uniprot IDs for given chromosome position Hi, Is there a way to get the knownGene table cross-referenced with hg19.kgXref (so that I can access the gene names) in GTF format? Thanks, Shobha. On Fri, Jun 11, 2010 at 11:43 AM, Antonio Coelho <[email protected]> wrote: > Hello Shobha, > > You can access this data by using the knownGene table in conjuction with the > kgXref table in our Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables) > > Select the 'Genes and Gene Prediction tracks' group, the 'UCSC Genes' track, > and 'knownGene' table. > Select the genomic region you want data from in the position box. You can > define multiple genomic regions by clicking 'define regions'. > Change the output format to 'selected fields from primary and related > tables', and click 'get output'. > This will take you to a new screen. Go the the section titled ' hg19.kgXref > fields' > Select kgID and spID from this section, and any other you may want, such as > gene name, position, or strand from the knownGene section. > Press 'Get output' near the top of the page. > > I hope this gets you what you need. Please contact us again with further > inquiries. > > Best > Antonio Coelho > UCSC Genome Bioinformatics Group > > > > Shobha Potluri wrote: >> >> Hi, >> I am trying to obtain the uniprot ids of the proteins >> corresponding to all knownGenes for a given chromosome position. >> Kindly point me to which tables of the UCSC database I would need to >> download in order to get this. >> >> Thanks a lot, >> Shobha. >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> > > -- Shobha. _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
