Hi ib, I just tried following the steps in the previously-answered question you found, and they work fine and appear to do what you want. If you want to use different GO identifiers for your filter, you should consult the Gene Ontology site (http://www.geneontology.org/, also linked in that post).
If you have further questions, please contact us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 7/20/12 2:42 PM, i b wrote: > From: i b <[email protected]> > Date: Fri, Jul 20, 2012 at 8:16 PM > Subject: Re: [Genome] UCSC tools > To: Luvina Guruvadoo <[email protected]> > > > hi i found this old post which explains how to do it for membrane > proteins which are those i need? > > https://lists.soe.ucsc.edu/pipermail/genome/2012-May/029297.html > > anyone has ever used it? > > On Fri, Jul 20, 2012 at 7:13 PM, Luvina Guruvadoo <[email protected]> wrote: >> 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 > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
