The data files ("UCSC Chain Files") in this directory are property of The Regents of the University of California, and made available free for non-commercial use by Independent Researchers and Nonprofit Organizations. Any other use of UCSC Chain Files requires a commercial license, for which users should contact firstname.lastname@example.org. As used herein, "Independent Researcher" means an individual who is autonomous with respect to the research activities for which he or she uses the UCSC Chain Files (note: such use does not extend to any use of the UCSC Chain Files at the direction and/or for the benefit of a for-profit organization); and "Nonprofit Organization" means a university or other institution of higher education, or a not-for-profit organization officially recognized or qualified under the laws of the country in which it is organized or located, or any nonprofit scientific or educational organization qualified under a federal, state or local jurisdiction's nonprofit organization statute. Downloading or using UCSC Chain Files indicates your acceptance of the End User License Agreement (EULA) posted at "https://genome.ucsc.edu/license/EULA.pdf"; redistribution of UCSC Chain Files by you must include this README file with these license restrictions, in the same archive or directory with the chain files. This directory contains the data files required as input to the liftOver utility. This tool -- which requires a Linux platform -- allows the mass conversion of coordinates from one assembly to another. The executable file for the utility can be downloaded from http://hgdownload.soe.ucsc.edu/admin/exe/ The file names reflect the assembly conversion data contained within in the format <db1>To<Db2>.over.chain.gz. For example, a file named hg15ToHg16.over.chain.gz file contains the liftOver data needed to convert hg15 (Human Build 33) coordinates to hg16 (Human Build 34). If no file is available for the assembly in which you're interested, please send a request to the genome mailing list (email@example.com) and we will attempt to provide you with one. To download a large file or multiple files from this directory, we recommend that you use ftp rather than downloading the files via our website. To do so, ftp to hgdownload.soe.ucsc.edu (user: anonymous), then cd to goldenPath/wuhCor1/liftOver. To download multiple files, use the "mget" command: mget <filename1> <filename2> ... - or - mget -a (to download all the files in the directory) ------------------------------------------------------- Please refer to the credits page (http://genome.ucsc.edu/goldenPath/credits.html) for guidelines and restrictions regarding data use for these assemblies. ------------------------------------------------------- Alternate methods to ftp access. Using an rsync command to download the entire directory: rsync -avzP rsync://hgdownload.soe.ucsc.edu/goldenPath/wuhCor1/liftOver/ . For a single file, e.g. wuhCor1ToHg19.over.chain.gz rsync -avzP rsync://hgdownload.soe.ucsc.edu/goldenPath/wuhCor1/liftOver/wuhCor1ToHg19.over.chain.gz . (Hg19 is merely an example here, not necessarily existing.) Or with wget, all files: wget --timestamping 'ftp://hgdownload.soe.ucsc.edu/goldenPath/wuhCor1/liftOver/*' With wget, a single file: wget --timestamping 'ftp://hgdownload.soe.ucsc.edu/goldenPath/wuhCor1/liftOver/wuhCor1ToHg19.over.chain.gz' -O wuhCor1ToHg19.over.chain.gz To uncompress the *.chain.gz files: gunzip <file>.chain.gz The liftOver utility can read the files in their .gz format, it is not necessary to uncompress them to use with the liftOver command.
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