Hi Jeremy, We're sorry that we haven't been able to point you to the data in the format you are expecting. If you can tell me the exact format you are looking for, I will be able to give you more detailed instructions.
If you are looking for particular regions within the genome, I recommend using the Table Browser, as my colleague mentions below. To do this, make the following selections: clade: Mammal genome: Human assembly: hg19 group: Mapping and Sequencing Tracks track: Mapability table: select the appropriate table (i.e., wgEncodeCrgMapabilityAlign24mer) output format: select your desired output format Click 'get output'. If you selected data points as your output format, your results would look something like this: chr1 10000 10090 0.000668896 chr1 10090 10091 0.000847458 chr1 10091 10093 0.00107411 ... Alternatively, the files are available for download here: http://genome.ucsc.edu/cgi-bin/hgFileUi?db=hg19&g=wgEncodeMapability These download pages can be found for any ENCODE track by clicking the "download" link located in the upper right corner of the ENCODE track description page. These files are in bigWig format, so you would have to extract the data using one of our utilities. See "Extracting Data from the bigWig Format" section here: http://genome.ucsc.edu/goldenPath/help/bigWig.html. I hope this helps clarify things for you. Please contact us again at [email protected] if you have any further questions. --- Luvina Guruvadoo UCSC Genome Bioinformatics Group On 4/24/2012 1:56 PM, Harris, Jeremy wrote: > Hello, > > I am trying to get ahold of the position based scores from the CRG Align > tracks. I have checked your database download page and all I can come up > with is a sql query. How can I get the complete track information? Thanks > for your time. Please don't link me back to your database download page, my > last two emails from your tech team pointed me there however I am no closer > to getting this data. > > Thanks! > > Jeremy Harris > Bioinformatic Analyst > Human and Molecular Genetics Center > Medical College of Wisconsin > Email: [email protected] > > -----Original Message----- > From: Luvina Guruvadoo [mailto:[email protected]] > Sent: Tuesday, April 24, 2012 2:37 PM > To: Harris, Jeremy > Cc: [email protected] > Subject: Re: [Genome] GEM Library > > Hi Jeremy, > > Yes, these files are available on our downloads server located here: > http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/ > > Please contact us again at [email protected] if you have any further > questions. > > --- > Luvina Guruvadoo > UCSC Genome Bioinformatics Group > > > On 4/24/2012 12:04 PM, Harris, Jeremy wrote: >> Are the CRG Align tracks available to download in their entirety? I have >> been looking but don't see them. >> >> Thanks for your time. >> >> Jeremy Harris >> Bioinformatic Analyst >> Human and Molecular Genetics Center >> Medical College of Wisconsin >> Email: [email protected] >> >> From: Greg Roe [mailto:[email protected]] >> Sent: Monday, April 23, 2012 5:39 PM >> To: Harris, Jeremy >> Cc: [email protected] >> Subject: Re: [Genome] GEM Library >> >> Hi Jeremy, >> >> We have to tracks, Burge RNA-seq and Mapability, which have been processed >> with GEM. If you want files from these, go to the Table Browser >> (http://genome.ucsc.edu/cgi-bin/hgTables). You'll find (under hg19) Burge >> RNA-seq in the Expression group and Mapability in the Mapping and Sequencing >> Tracks group. >> >> You can always looks things like this up by clicking the "track search" >> button in the Genome Browser and searching for "GEM". >> >> >> Please let us know if you have any additional questions: >> [email protected]<mailto:[email protected]> >> >> - >> Greg Roe >> UCSC Genome Bioinformatics Group >> >> On 4/23/12 11:45 AM, Harris, Jeremy wrote: >> >> Hello, >> >> >> >> I am curious if you guys have downloadable results sets for HG18/HG19 that >> are processed with GEM Library. Let me know. >> >> >> >> Thanks! >> >> >> >> Jeremy Harris >> >> Bioinformatic Analyst >> >> Human and Molecular Genetics Center >> >> Medical College of Wisconsin >> >> Email: [email protected]<mailto:[email protected]> >> >> >> >> _______________________________________________ >> >> Genome maillist - [email protected]<mailto:[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
