Hello, Please note step 8 in the email from my colleague below:
8. In the "go.term based filters" section, enter exactly the following in the "Free-form query" box: name like "%cytoplasm%" It appears you have typed the query in the go.goaPart field instead of go.term. Also, you must type in the query exactly as it is above: name like "%cytoplasm%" Please contact us again at [email protected] if you have any further questions. --- Luvina Guruvadoo UCSC Genome Bioinformatics Group On 7/19/2012 2:40 PM, i b wrote: > ok, > so I have done everything step by step and got this message: > --------------------------------------------------------------------------- > Can't start query: > select goId,dbObjectId from goaPart where (%surface%) > > --------------------------------------------------------------------------- > --------------------------------------------------------------------------- > mySQL error 1064: You have an error in your SQL syntax; check the > manual that corresponds to your MySQL server version for the right > syntax to use near '%surface%)' at line 1 > --------------------------------------------------------------------------- > > > heeeeeeeelp > ib > > On Thu, Jul 19, 2012 at 9:14 PM, i b<[email protected]> wrote: >> HI Steve, >> thanks very much for the instructions. >> >> HoweverI had a problem since after sending the output to galaxy from >> the table, I couldn't find the filter as written in step 3. >> the page i was directed to has three tables with the following titles: >> 1.Select Fields from hg19.knownGene >> 2.hg19.kgXref fields >> 3.Linked Tables >> >> I could not read in anywhere the "filter" line, and the "create" button. >> >> Regards, >> 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
