Hi, That info was tremendously useful. I got what I wanted very easily! Thanks a lot.
Blessed Holidays, Joses -----Original Message----- From: Brooke Rhead [mailto:[email protected]] Sent: Wed 24-Dec-08 08:40 To: Joses HO Wei-Hao Cc: [email protected] Subject: Re: [Genome] Extracting Gene Information from Gene Description and Page Index Hello Joses, You can get the RefSeq summary displayed on the UCSC Genes details page from the hg18.refSeqSummary.summary field. You can get the short description from the hg18.kgXref.description field. I can tell you how to go about getting this information for a genomic region via the Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables). Select the UCSC Genes track and the knownGene table. Enter the position you wish to get data for in the position box. Choose "output format: selected fields from primary and related tables". Hit "get output". On the next page, choose to allow selection from the kgXref and knownToRefSeq tables (you need the second one to get to the refSeqSummary table). After hitting the button at the bottom of the page, you should see the refSeqSummary table listed in the "linked tables" section. Select it as well. Now you should have four tables selected: knownGene, kgXref, knownToRefSeq and refSeqSummary. Choose at least one field from knownGene, then choose hg18.kgXref.description and hg18.refSeqSummary.summary fields. Now hit "get output" at the top of the page. You should have the description and RefSeq summaries for all of the UCSC Genes in the range you specified. -- Brooke Rhead UCSC Genome Bioinformatics Group On 12/23/08 3:56 AM, Joses HO Wei-Hao wrote: > Hello, > > I would like to extract relevant info from the Gene Description and Page Index (e.g. the one here <http://genome.ucsc.edu/cgi-bin/hgGene?hgg_gene=uc002yif.2>). > > Is there a way I can use a SQL query to extract desired fields, say for instance the gene description and RefSeq summary, for all UCSC known Genes within a specified genomic region? > Many thanks, and merry Christmas! > 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
