Hi Jeremy, The data in the Mapability subtracks are in bigWig format, which is binary. You will need to use one of our utilities to convert the data into a text format. Please see the very last section on this page: http://genome.ucsc.edu/goldenPath/help/bigWig.html, titled, "Extracting Data from the bigWig Format ".
You can use the utilities described there and the URLs to the bigWig (.bw/.bigwig) files to convert them in to formats you will find more useful. To get the URLs you are interested in, go to: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/, right-click on a file and use "Copy Link Location" (or similar for your OS/Browser). You can then paste the link/URL to that file into the command line to use with one of the bigWigTo* utilities. To convert to wig, for example, you'd run: [...]$ bigWigToWig in.bigWig out.wig ...where: in.bigWig = the url to the bigWig file (e.g., ) out.wig = the file you want to save the output to Please let us know if you have any additional questions: [email protected] - Greg Roe UCSC Genome Bioinformatics Group On 4/25/12 8:21 AM, Harris, Jeremy wrote: > Hello, > > I am trying to figure out if there is a way that I can download all > chromosomes of the track CRG Align tracks since it was processed using GEM. > I have tinkered with the table browser but the limit of 10 million results > makes it impractical to get a genome worth of the chromosome, position, and > score information for everything. Typically when I need this type of > information I use your "Full Data Set" but as this is a track it isn't > turning out quite so easy. I have gone to the Annotation Database from your > download section; however the only available download they have for this > track is a sql query. What I am hoping and trying to get is a tab delimited > (Or something I can shape into a tab delimited) file with the chromosome, > position, and score information. If there is anything you guys can do to > help I would appreciate it. If the answer to getting this information is a > sql query that I write into a perl script to query your system (which I have > experience in querying! y! > our system from scripts) then that is an acceptable solution as well. > > Thanks for your help. > > Jeremy Harris > Bioinformatic Analyst > Human and Molecular Genetics Center > Medical College of Wisconsin > Email: [email protected] > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
