Sorry, I meant to paste an example URL in below, such as: in.bigWig = the url to the bigWig file (e.g., http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/wgEncodeCrgMapabilityAlign75mer.bigWig)
On 4/25/12 1:59 PM, Greg Roe wrote: > 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 queryin! g! > 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
