Hi Greg, The table schema is the best place to look for table field descriptions. You can access the table schema either through the table browser (http://genome.ucsc.edu/cgi-bin/hgTables), or through the track description page, which for refSeq on hg19 is here: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=refGene. Here is a direct link to the table schema for your table: http://genome.ucsc.edu/cgi-bin/hgTables?db=hg19&hgta_group=genes&hgta_track=refGene&hgta_table=refGene&hgta_doSchema=describe+table+schema.
I hope this information is helpful. Please feel free to contact the mail list again if you require further assistance. Best, Mary ------------------ Mary Goldman UCSC Bioinformatics Group On 8/23/10 9:57 AM, Gregory Dougherty wrote: > Thank you, Mary. Did it, and now everything is in there. > > One question: where would I find a description of the fields? I.E. what's > the difference between txStart and cdsStart, txEnd and cdsEnd? > > Thanks! > > Greg > > ----- Original Message ----- > From: "Mary Goldman"<[email protected]> > To: "Gregory Dougherty"<[email protected]> > Cc: [email protected] > Sent: Friday, August 20, 2010 7:05:22 PM GMT -06:00 US/Canada Central > Subject: Re: [Genome] Map RefSeq IDs to genome positions > > Hi Greg, > > There are no special restrictions for using our blat-mapped RefSeq Genes. To > obtain a complete list of all of our mappings go to our downloads page > (http://hgdownload.cse.ucsc.edu/downloads.html), select your assembly of > interest and click on "Annotation database". From here, click to download > refGene.txt.gz (the data) and refGene.sql (the MySql commands needed to load > this data into a database). No join is needed; both the RefSeq IDs and their > chromosome coordinates are in refGene.txt.gz. > > I hope this information is helpful. Please feel free to contact the mail > list if you require further assistance. > > Best, > Mary > ------------------ > Mary Goldman > UCSC Bioinformatics Group > > ----- Original Message ----- > From: "Gregory Dougherty"<[email protected]> > To: [email protected] > Sent: Friday, August 20, 2010 12:09:12 PM GMT -08:00 US/Canada Pacific > Subject: [Genome] Map RefSeq IDs to genome positions > > I need to build a fairly comprehensive list of mappings of human RefSeq IDs > to chromosome positions. As the Genome Browser appears to have this data, I > figured I would start here. > > 1: Are there any special restrictions on using the mapping data? > 2: Assuming there aren't, what's the easiest way for me to create a local DB > of those mappings? Is there a Jim Kent tool that I missed? Can I simply > load a couple of data files into MySQL and do a Join? > > TIA, > > Greg > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
