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 email@example.com. 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. 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.cse.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 (firstname.lastname@example.org) and we will attempt to provide you with one. ERROR NOTE: We have determined that UCSC's assembly of the chrUn sequence for oryLat1 is incorrect: the gap relationships between contigs within their ultracontigs are broken. We are in the process of correcting this error, and plan to post a corrected data set in late July. We apologize for the inconvenience. 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.cse.ucsc.edu (user: anonymous), then cd to goldenPath/oryLat1/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.
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