Hello, The track descriptions are contained in the mySQL database in the table "<db>.trackDb.html". An query against the public mySQL server to retrieve this data from the Human Mar. 2006 (hg18) assembly would look like this:
$ mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e "select tableName, html from trackDb;" hg18 >& output_list http://genome.ucsc.edu/FAQ/FAQdownloads#download29 Good luck and please let us know if you need more help, Jennifer Jackson UCSC Genome Bioinformatics Group Asmann, Yan W., Ph.D. wrote: > Thanks Jennifer. > I am working to intersect with the tracks in batch. So the schema in SQL > files works for me. > > I have another questions. On your web site, I can go to a schema web > page (e.g. http://genome.ucsc.edu/cgi-bin/hgTables). The web page > provides a more human understandable name for each table For example, > table name multiz17way is not so readable, but the description in the > schema web page provides information about the table: "This track shows > a measure of evolutionary conservation in 17 vertebrates, including > mammalian, amphibian, bird, and fish species, based on a phylogenetic > hidden Markov model, phastCons (Siepel et al., 2005). Multiz alignments > of the following assemblies were used to generate this track". > > So, is there a place that I can download the descriptions in bulk? > > Thank you so much for your helps!! > 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: Jennifer Jackson [mailto:[email protected]] > Sent: Tuesday, June 16, 2009 6:59 PM > To: Asmann, Yan W., Ph.D. > Cc: Kayla Smith; [email protected] > Subject: Re: [Genome] Genomic Regions of Interest > > 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
