Good Morning Justin: You can use our utility program: hgWiggle to extract this data from the two files that you can download and have locally:
ftp://hgdownload.cse.ucsc.edu/gbdb/hg18/wib/uwNucOccA375.wib ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/uwNucOccA375.txt.gz See the instructions at: http://genomewiki.ucsc.edu/index.php/Using_hgWiggle_without_a_database --Hiram >> From: "Justin Fincher" <[email protected]> >> To: "Jennifer Jackson" <[email protected]> >> Cc: [email protected] >> Sent: Thursday, September 10, 2009 10:58:32 AM GMT -08:00 US/Canada Pacific >> Subject: Re: [Genome] building MySQL queries (examples or techniques) >> >> Thank you so much for your help. I do have a specific question that >> I >> was hoping you could help me with. I am trying to pull values for >> different ranges from the uwNucOccA375 table. From the description, >> it seems that I can't pull the individual values for a range, but >> must >> do it myself from the data file. Is this correct? And if it is, >> could you help me with the absolute path for the file designated in >> the table? It gives a relative path, but I'm not sure how to >> actually >> access the file. Thank you again for your help. >> >> - Fincher >> >> >> On Wed, Sep 2, 2009 at 16:54, Jennifer Jackson <[email protected]> >> wrote: >>> Hello, >>> >>> The queries for the Table browser can all be recreated in regular >> SQL, but the method used by the Table browser will not always be most >> desirable query for a user. However, the schema information provided >> by the Table browser will definately be necessary when constructing >> your own query. For our example, I am assuming that you are using our >> public mySQL server (not Oracle or Sybase which have their own >> syntax). >>> For mySQL syntax, try a google search. There are several good >> sites. >>> To learn the table structure, using the Table browser, bring up the >> track of interest. The default table is the primary table. Click on >> the view schema button next to the table. This page has three >> components. Top = the table schema with examples and data definitions. >> Middle = Linked tables, the actual table name and the key (field) to >> link between in the "where" clause of your mySQL statement. Bottom = >> (For primary tables only) The track description. >>> The middle tables are interactive, meaning that you can click on >> them to view their schema and related tables below. >>> A general query would be something like this: >>> >>> select >>> Â table1.field1, >>> Â table3.field2 >>> from >>> Â table1, >>> Â table3 >>> where >>> Â table1.field3 = table2.field4; >>> >>> The select and from clauses are required. The where clause is >> optional but is where the actual filtering or joining between data >> keys occurs. This can get complicated. Then there are all sorts of >> other options, "sort by" and such. There are rules for using quotes >> and rules for when a "=" should be used (for numbers) rather than an >> "equal to" should be used (for non-numbers). Wildcards are possible in >> some types of matches. And of course the whole thing can be wrapped up >> into a shell, perl, c or other script with the right libraries >> installed. >>> Here is the link to our public server mySQL help page, that includes >> some help regarding set up: >> http://genome.ucsc.edu/FAQ/FAQdownloads#download29 >>> If you find yourself stuck with a particular query, we can offer >> some help to fine tune or offer advice, >>> Thanks, Jennifer >>> >>> >>> ------------------------------------------------ >>> Jennifer Jackson >>> UCSC Genome Bioinformatics Group >>> >>> ----- "Justin Fincher" <[email protected]> wrote: >>> >>>> From: "Justin Fincher" <[email protected]> >>>> To: [email protected] >>>> Sent: Wednesday, September 2, 2009 11:55:49 AM GMT -08:00 US/Canada >> Pacific >>>> Subject: [Genome] building MySQL queries (examples or techniques) >>>> >>>> Pardon if this is a remedial question, but I am just getting >> started >>>> working with using MySQL queries to extract information from the >>>> database. I was wondering if there was a resource with some >> example >>>> queries or if there was a basic "formula" for understanding how to >>>> convert what is done in the table browser to a database query. Â I >>>> only >>>> have a little experience with MySQL and am finding browsing >> through >>>> the tables to be less beneficial than I would hope. Â Thank you for >>>> your help. >>>> >>>> - Fincher _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
