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
