Hello Joses, You can use the Table Browser in a slightly different manner to get the exon coordinates for the genes in the knownCanonical table.
In the Table Browser, select the UCSC Genes track, and then select the knownCanonical table from the drop-down menu. Choose "output format: selected fields from primary and related tables" and hit "get output". On the next page, select the knownGene table from the "Linked Tables" list and hit the "Allow Selection From Checked Tables" button. Choose at least one field from the knownCanonical table (such as "transcript"), and then choose the fields you wish to retrieve from the knownGene table. Hit "get output". You should get only the rows from the knownGene table that correspond to the genes in the knownCanonical table. I hope this is helpful. If you have further questions, please feel free to write back to [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group Joses HO Wei-Hao wrote: > Hi, > > Thanks for the help, but my query doesn't seem to work. > > Using the filter option from the Table Browser Page, I attempt to get the > knownGenes table without all the splice variants listed by using the > free-form query "name!=hg18.knownCanonical.transcript". > > However I get the following errors: > > --------------------------------------------------------------------------- > Can't start query: > select > name,chrom,strand,txStart,txEnd,cdsStart,cdsEnd,exonCount,exonStarts,exonEnds,proteinID,alignID > from knownGene where chrom='chr19' and txStart<63811651 and txEnd>53014479 > and (name!=knownCanonical.transcript) order by txStart > > --------------------------------------------------------------------------- > --------------------------------------------------------------------------- > mySQL error 1109: Unknown table 'knownCanonical' in where clause > --------------------------------------------------------------------------- > > and > > --------------------------------------------------------------------------- > Can't start query: > select > name,chrom,strand,txStart,txEnd,cdsStart,cdsEnd,exonCount,exonStarts,exonEnds,proteinID,alignID > from knownGene where chrom='chr19' and txStart<63811651 and txEnd>53014479 > and (name!=hg18.knownCanonical.transcript) order by txStart > > --------------------------------------------------------------------------- > --------------------------------------------------------------------------- > mySQL error 1109: Unknown table 'hg18.knownCanonical' in where clause > --------------------------------------------------------------------------- > > Any ways to fix this? > > Thanks, > Joses > > > -----Original Message----- > From: Kayla Smith [mailto:[email protected]] > Sent: Fri 19-Dec-08 05:57 > To: Joses HO Wei-Hao > Cc: [email protected] > Subject: Re: [Genome] Extracting exon lengths and coordinates from Table > Browser > > > Joses, > > Our hg18.knownCanonical table might be what you're looking for. This > table describes the canonical splice variant of a gene. > > Please see this previously answered mailing list question: > http://www.soe.ucsc.edu/pipermail/genome/2008-January/015274.html > > I hope this is helpful to you. Please don't hesitate to contact us > again if you require further assistance. > > Kayla Smith > UCSC Genome Bioinoformatics Group > > > Joses HO Wei-Hao wrote: >> Hi, >> >> I have a genomic region of interest, and I want to extract all the exon >> coordinates for sequence capture. The annotation database I want to use is >> the UCSC Known Genes database. >> >> However, it seems to me that the Known Genes database contains splice >> variants for several genes. I just want the start and stop coordinates of >> all exons (both coding and non-coding, and both known and novel) within my >> region of interest, without any duplicated exons. Any idea on how this can >> be done? >> >> Thanks, >> Joses >> _______________________________________________ >> Genome maillist - [email protected] >> http://www.soe.ucsc.edu/mailman/listinfo/genome > > > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
