Hello, The Table Browser is a good tool for understanding what tables are associated with a track and how they are related. http://genome.ucsc.edu/cgi-bin/hgTables
This is the UCSC Genes track. So, open the Table browser, navigate to the track, then with the primary table (default table knownGene) selected, click on the button "describe table schema". Note that some tables will link to other top level databases such as hgFixed, which would be important to know when accessing the data via SQL. Some of the data my not be in the tables, but rather is a special set of files that the table's reference by file name. These files are contained in the directory we call /gbdb/<db>/. These should be downloaded using ftp/rsync. Follow the basic download instructions, but instead of going into /goldenPath once connected, go into gbdb instead. The path given in the tables will show you which files to collect. You could at this point download the tables as well (/goldenPath/<db>/database (.txt.gz files are the data, .sql is the mySQL schema). General download instructions: http://genome.ucsc.edu/FAQ/FAQdownloads.html#download1 We hope this helps, but please let us know if you need more help, Jennifer --------------------------------- Jennifer Jackson UCSC Genome Bioinformatics Group http://genome.ucsc.edu/ On 2/16/10 10:53 AM, Bizzy Tran wrote: > Hi, > > > > I did a search on the Genomes page using the ID uc003imv and the website > took me to the browser page for that gene > (http://genome.ucsc.edu/cgi-bin/hgTracks?org=Mouse > <http://genome.ucsc.edu/cgi-bin/hgTracks?org=Mouse&db=hg18&position=uc003imv > .1> &db=hg18&position=uc003imv.1). Then I clicked on the bar under the title > "UCSC Genes Based on RefSeq, UniProt, GenBank, CCDS and Comparative > Genomics" and was taken to this page > http://genome.ucsc.edu/cgi-bin/hgGene?hgg_gene=uc003imv.2 > <http://genome.ucsc.edu/cgi-bin/hgGene?hgg_gene=uc003imv.2&hgg_prot=&hgg_chr > om=chr4&hgg_start=153676865&hgg_end=153679864&hgg_type=knownGene&db=hg18&hgs > id=152071858> > &hgg_prot=&hgg_chrom=chr4&hgg_start=153676865&hgg_end=153679864&hgg_type=kno > wnGene&db=hg18&hgsid=152071858. I am interested in getting all the > information from the Gene Model Information table on that page using SQL but > I am unsure which tables I should be searching through. The information that > I am talking about is put into a list on this page: > http://genome.ucsc.edu/cgi-bin/hgGene?hgg_do_txInfoDescription=1 > <http://genome.ucsc.edu/cgi-bin/hgGene?hgg_do_txInfoDescription=1&hgsid=1520 > 71858> &hgsid=152071858. Can you please let me know which tables I should be > looking at? > > > > Also, is the txCDsPredict score calculated in real time or can I retrieve > from a table in the database? I ran the following query, SELECT * FROM > `information_schema`.`COLUMNS` WHERE COLUMN_NAME like '%predict%' to look > for the txCdsPredict score column but had no luck. > > > > Thanks. Your help would be much appreciated. > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
