On 01.08.11 04:27, Brooke Rhead wrote: > 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 >
Thanks a lot guys for your fast reply. All your suggestion are very useful. C. _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
