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
