Hi, I have a question regarding refFlat.txt file. I assume it is generated using NCBI RefSeq's refseqgene.genomic.gbff file? How often is the refFlat.txt file updated? If it's not from the refseqgene.genomic.gbff file, which source file did you use?
Is it possible to get the script or code for the extraction of refFlat.txt from the source file? Thank you!! Yan >Yan Asmann, Ph.D. | Assistant Professor of Medical Informatics | Division of Biomedical Statistics and Informatics | Department of Human Sciences Research | Mayo 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: Friday, June 19, 2009 2:15 PM To: Asmann, Yan W., Ph.D. Cc: Kayla Smith; [email protected] Subject: Re: [Genome] Genomic Regions of Interest 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
