sorry steve, I found the filter button.My mistake! ib
On Thu, Jul 19, 2012 at 8:18 PM, Steve Heitner <[email protected]> wrote: > Hello. > > Based on what you've described, it sounds like you would like to get a > listing of genes that is filtered based on gene ontology. You can do this > using our Table Brower. If you're unfamiliar with the Table Browser, please > see the User's Guide at > http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html. > > Perform the following steps: > > 1. In your browser, go to http://genome.ucsc.edu/cgi-bin/hgTables > > 2. Set the following options: > Clade: Mammal > Genome: Human > Assembly: Feb. 2009 (GRCh37/hg19) > Group: Genes and Gene Prediction Tracks > Track: UCSC Genes > Table: knownGene > Region: genome > Output format: selected fields from primary and related tables (you can also > check the "Galaxy" checkbox on this line to send your output to Galaxy) > > 3. Next, you will need to create a filter that will list only the results > you're looking for. On the "filter" line, click the "create" button. > > 4. Scroll down to the "Linked Tables" section and check the "go.goaPart" > checkbox. > > 5. Scroll to the bottom of the page and click the "allow filtering using > fields in checked tables" button. > > 6. Scroll down to the "Linked Tables" section and check the "go.term" > checkbox. > > 7. Repeat step 5. > > 8. In the "go.term based filters" section, enter exactly the following in > the "Free-form query" box: name like "%cytoplasm%" > > 9. Click the "submit" button. > > 10. Click the "get output" button. > > 11. Repeat steps 4-7. > > 12. In the "Select Fields from hg19.knownGene" section, check the checkboxes > of the fields you would like to include in your output. > > 13. In the "go.term fields" section, check the "name" checkbox. > > 14. Click the "get output" button (or the "done with selections" button if > sending to Galaxy). > > Note that in step 8, the term you enter between the % symbols is whatever > term you are trying to filter. If you enter %cytoplasm% as listed in step > 8, any record that contains "cytoplasm" anywhere in that field will appear > in your output. You can revise your filter term based on your desired > output. > > Please contact us again at [email protected] if you have any further > questions. > > --- > Steve Heitner > UCSC Genome Bioinformatics Group > > -----Original Message----- > From: [email protected] [mailto:[email protected]] On > Behalf Of i b > Sent: Tuesday, July 17, 2012 2:06 PM > To: [email protected]; [email protected] > Subject: [Genome] UCSC tools > > Hi, > is there a way to create a job in my galaxy history from UCSC genome browser > that contains a specific set of genes encoding for example only for nuclear > or cytoplasmatic proteins proteins? > How can I do that? > > Thanks a lot! > ngs-ib > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
