Hello Yan, If data came from:
http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/ Then the schema information is in two locations: - Table browser - bring up the table and click on "describe table schema" - Downloads - for each file *.txt.gz there is a schema in *.sql Thanks, Jennifer Jackson UCSC Genome Bioinformatics Group Asmann, Yan W., Ph.D. wrote: > Hi Kayla, > I downloaded all the txt.gz data from the ftp site. I am writing my own > script to exact information from each table. But I just realized that I > need table schema for each of the tables. Where can I download this > information at one place? > > Thank you very much for your help! > Yan > > > >> Yan Asmann, Ph.D. | Assistant Professor of Medical Informatics | >> > Division of Biomedical Statistics and Informatics| College of Medicine | > 507-266-6818 | Fax: 507-284-0360 | [email protected] > >> Mayo Clinic | 200 First Street SW | Rochester, MN 55905 | >> > www.mayoclinic.org > > > -----Original Message----- > From: Kayla Smith [mailto:[email protected]] > Sent: Thursday, May 28, 2009 6:20 PM > To: Asmann, Yan W., Ph.D. > Cc: [email protected] > Subject: Re: [Genome] Genomic Regions of Interest > > > Hello Yan, > > The approach I would take to this problem is to first create a "Custom > Track" of your regions of interest, and then intersect existing > annotation tracks with that Custom Track. > > Here is some information on custom tracks, > http://genome.ucsc.edu/cgi-bin/hgCustom > http://genome.ucsc.edu/goldenPath/help/customTrack.html > > Or if you'd like to download data and write your own scripts to search > through it, here is our downloads page for hg18 (sometimes takes awhile > to load): > http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/ > > Please note that the Galaxy website has some kind intersection tools as > well: > http://main.g2.bx.psu.edu/ > > I hope some of these tools will be useful to you. Please don't hesitate > to contact us again if you require further assistance. > > Kayla Smith > UCSC Genome Bioinformatics Group > > ----- "Yan W. Asmann, Ph.D." <[email protected]> wrote: > > >> Hi, >> I am interested in finding out all features of particular genomic >> regions. One way to do this is by looking at all overlapping Genome >> Browser Tracks. To do this at the interactive web browser, I'd have >> to >> look at one track or several tracks at a time. Is there a better way >> of >> doing this? >> >> Is there an option to download data for all tracks, so I can write a >> script to search for tracks overlapping with my regions of interest? >> >> Thanks! >> Yan >> >> >> >> >> _______________________________________________ >> 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
