Hi Carsten and Thomas, Another option for converting from psl format (which is what the SQL dump download consists of for the EST tracks) to BED format is the command line tool pslToBed, available as part of the Genome Browser source tree:
http://hgdownload.cse.ucsc.edu/admin/jksrc.zip instructions for building from source are here (note that you do not need to do every step if you are only building this tool): http://genome.ucsc.edu/admin/jk-install.html Also note the instructions on the download page for alternatives to http access for downloading large files. The xenoEst file for hg19 is 1.2 Gb. -- Brooke Rhead UCSC Genome Bioinformatics Group Thomas Juettemann wrote on 7/31/11 4:11 PM: > Hello Bob, > > Thanks for the quick answer, especially on a Sunday! > Downloading the SQL dump only solves part of the problem, as one still > needs to convert to BED or any other format. > > I found that exporting the table browser results to Galaxy and then > downloading the import works very well. > > Cheers, > Thomas > > On Mon, Aug 1, 2011 at 00:47, robert kuhn<[email protected]> wrote: >> Should go to the downloads page and download entire file >> instead of using Table Browser. >> >> http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/ >> >> regards, >> >> --b0b kuhn >> ucsc genome bioinformatics group >> >> On 7/31/2011 3:30 PM, Thomas Juettemann wrote: >>> >>> Hi all, >>> >>> I tried the same and I think he is right, the resulting file is too >>> big as my connection times out as well. >>> >>> Clade: Mammal >>> Genome: Human >>> Assembly: hg19 >>> group: mRNA and EST >>> region: genome >>> output: BED >>> -->get Output >>> Create one BED record per: Whole alignment. >>> -->get Bed >>> >>> Some results are displayed, but not all (loading stops). >>> >>> Cheers, >>> Thomas >>> >>> On Sun, Jul 31, 2011 at 16:25, Carsten Raabe<[email protected]> >>> wrote: >>>> >>>> Dear Madame, dear Sir, >>>> >>>> my name is Carsten and I am working at the institute of experimental >>>> Pathology at Muenster University in Germany. I would like to download a >>>> BED formated text-file that contains all human exon EST coordinates >>>> (including its orientation) via the table browser. I tried so using the >>>> table browser options, however I failed. Could you please suggest what >>>> would be the appropriate way accessing the data. In addition I would >>>> like to download the (>>> human) Other EST file but I expect the very >>>> same problem. ( I guess it is connected with the file size itself) >>>> >>>> Thanks in advance, >>>> >>>> C. >>>> _______________________________________________ >>>> 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
