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 genomebrowser@ucsc.edu. 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 (genome@soe.ucsc.edu) 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/mm39/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/mm39/liftOver/ . For a single file, e.g. mm39ToHg19.over.chain.gz rsync -avzP rsync://hgdownload.soe.ucsc.edu/goldenPath/mm39/liftOver/mm39ToHg19.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/mm39/liftOver/*' With wget, a single file: wget --timestamping 'ftp://hgdownload.soe.ucsc.edu/goldenPath/mm39/liftOver/mm39ToHg19.over.chain.gz' -O mm39ToHg19.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.
Name Last modified Size Description
Parent Directory - md5sum.txt 2024-11-04 16:07 4.9K mm39ToGCA_964188545.1.over.chain.gz 2024-10-30 15:39 14M mm39ToGCA_964188535.1.over.chain.gz 2024-09-04 12:29 2.8M mm39ToGCF_009806435.1.over.chain.gz 2024-06-28 14:28 50M mm39ToGCA_921999865.2.over.chain.gz 2024-06-24 22:12 3.4M mm39ToGCA_921997145.2.over.chain.gz 2024-03-28 08:44 6.9M mm39ToGCA_921998325.2.over.chain.gz 2024-02-09 16:15 7.3M mm39ToGCA_921997125.2.over.chain.gz 2024-01-21 15:56 7.2M mm39ToGCA_921999005.2.over.chain.gz 2024-01-18 07:46 15M mm39ToGCF_019923935.1.over.chain.gz 2024-01-10 14:15 53M mm39ToGCF_003121395.1.over.chain.gz 2023-06-05 03:48 53M mm39ToGCF_029281585.1.over.chain.gz 2023-05-30 06:44 68M mm39ToGCF_028858775.1.over.chain.gz 2023-05-30 05:41 68M mm39ToGCF_028885655.1.over.chain.gz 2023-05-30 00:26 68M mm39ToGCF_011764305.1.over.chain.gz 2023-05-29 23:02 57M mm39ToGCF_016699485.2.over.chain.gz 2023-05-29 16:48 4.6M mm39ToGCA_921998555.2.over.chain.gz 2023-04-12 12:04 7.4M mm39ToGCA_001624445.1.over.chain.gz 2023-04-08 07:44 19M mm39ToGCA_011100615.1.over.chain.gz 2023-03-17 22:44 66M mm39ToGCA_001624835.1.over.chain.gz 2022-10-30 08:07 13M mm39ToGCA_001624775.1.over.chain.gz 2022-10-30 03:44 20M mm39ToMm9.over.chain.gz 2022-10-25 14:53 206K mm39ToGCA_004027735.1.over.chain.gz 2022-10-11 01:21 54M mm39ToGCA_013030995.1.over.chain.gz 2022-03-21 20:05 4.9M mm39ToGCF_002742125.1.over.chain.gz 2021-12-21 20:50 52M mm39ToGCF_001704415.1.over.chain.gz 2021-12-09 19:25 53M mm39ToFelCat9.over.chain.gz 2021-12-09 18:43 60M mm39ToOviAri1.over.chain.gz 2021-12-09 17:37 32M mm39ToSusScr11.over.chain.gz 2021-09-24 13:18 55M mm39ToCanFam3.over.chain.gz 2021-09-24 12:51 58M mm39ToCanFam6.over.chain.gz 2021-05-18 11:41 58M mm39ToXenTro10.over.chain.gz 2021-02-23 01:56 3.8M mm39ToRn7.over.chain.gz 2021-02-04 18:08 73M mm39ToCavPor3.over.chain.gz 2020-11-25 21:46 58M mm39ToTupBel1.over.chain.gz 2020-11-25 21:31 44M mm39ToSpeTri2.over.chain.gz 2020-11-25 20:27 67M mm39ToSorAra2.over.chain.gz 2020-11-25 20:18 28M mm39ToOchPri3.over.chain.gz 2020-11-25 19:04 38M mm39ToMonDom5.over.chain.gz 2020-11-25 02:08 10M mm39ToXenTro9.over.chain.gz 2020-11-25 01:14 3.7M mm39ToDanRer11.over.chain.gz 2020-11-25 00:57 2.9M mm39ToGalGal6.over.chain.gz 2020-11-25 00:11 4.6M mm39ToEchTel2.over.chain.gz 2020-11-25 00:08 30M mm39ToLoxAfr3.over.chain.gz 2020-11-24 23:39 51M mm39ToPetMar3.over.chain.gz 2020-11-24 23:02 2.2M mm39ToOviAri4.over.chain.gz 2020-11-24 22:19 53M mm39ToOryCun2.over.chain.gz 2020-11-24 22:11 50M mm39ToNeoSch1.over.chain.gz 2020-11-24 21:46 62M mm39ToEriEur2.over.chain.gz 2020-11-24 21:33 29M mm39ToOtoGar3.over.chain.gz 2020-11-24 13:36 59M mm39ToSusScr3.over.chain.gz 2020-11-24 13:35 52M mm39ToTurTru2.over.chain.gz 2020-11-24 13:35 61M mm39ToEquCab3.over.chain.gz 2020-11-24 13:31 67M mm39ToPanPan3.over.chain.gz 2020-11-24 05:02 67M mm39ToGorGor6.over.chain.gz 2020-11-24 04:45 67M mm39ToPanTro6.over.chain.gz 2020-11-24 04:42 67M mm39ToGalVar1.over.chain.gz 2020-11-24 01:11 71M mm39ToManPen1.over.chain.gz 2020-11-23 23:48 56M mm39ToTarSyr2.over.chain.gz 2020-11-23 18:36 64M mm39ToBosTau9.over.chain.gz 2020-11-23 17:49 53M mm39ToRheMac10.over.chain.gz 2020-10-20 16:43 67M mm39ToRn6.over.chain.gz 2020-10-20 16:42 74M mm39ToCalJac4.over.chain.gz 2020-09-04 14:49 64M mm39ToHg38.over.chain.gz 2020-08-18 09:09 68M mm39ToCanFam5.over.chain.gz 2020-08-17 15:28 59M mm39ToMm10.over.chain.gz 2020-07-30 14:54 50K