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
mm39ToBosTau9.over.chain.gz 2020-11-23 17:49 53M
mm39ToCalJac4.over.chain.gz 2020-09-04 14:49 64M
mm39ToCanFam3.over.chain.gz 2021-09-24 12:51 58M
mm39ToCanFam5.over.chain.gz 2020-08-17 15:28 59M
mm39ToCanFam6.over.chain.gz 2021-05-18 11:41 58M
mm39ToCavPor3.over.chain.gz 2020-11-25 21:46 58M
mm39ToDanRer11.over.chain.gz 2020-11-25 00:57 2.9M
mm39ToEchTel2.over.chain.gz 2020-11-25 00:08 30M
mm39ToEquCab3.over.chain.gz 2020-11-24 13:31 67M
mm39ToEriEur2.over.chain.gz 2020-11-24 21:33 29M
mm39ToFelCat9.over.chain.gz 2021-12-09 18:43 60M
mm39ToGCA_001624445.1.over.chain.gz 2023-04-08 07:44 19M
mm39ToGCA_001624775.1.over.chain.gz 2022-10-30 03:44 20M
mm39ToGCA_001624835.1.over.chain.gz 2022-10-30 08:07 13M
mm39ToGCA_004027735.1.over.chain.gz 2022-10-11 01:21 54M
mm39ToGCA_011100615.1.over.chain.gz 2023-03-17 22:44 66M
mm39ToGCA_013030995.1.over.chain.gz 2022-03-21 20:05 4.9M
mm39ToGCA_921997125.2.over.chain.gz 2024-01-21 15:56 7.2M
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_921998555.2.over.chain.gz 2023-04-12 12:04 7.4M
mm39ToGCA_921999005.2.over.chain.gz 2024-01-18 07:46 15M
mm39ToGCA_921999865.2.over.chain.gz 2024-06-24 22:12 3.4M
mm39ToGCA_964188535.1.over.chain.gz 2024-09-04 12:29 2.8M
mm39ToGCA_964188545.1.over.chain.gz 2024-10-30 15:39 14M
mm39ToGCF_001704415.1.over.chain.gz 2021-12-09 19:25 53M
mm39ToGCF_002742125.1.over.chain.gz 2021-12-21 20:50 52M
mm39ToGCF_003121395.1.over.chain.gz 2023-06-05 03:48 53M
mm39ToGCF_009806435.1.over.chain.gz 2024-06-28 14:28 50M
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
mm39ToGCF_019923935.1.over.chain.gz 2024-01-10 14:15 53M
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_029281585.1.over.chain.gz 2023-05-30 06:44 68M
mm39ToGalGal6.over.chain.gz 2020-11-25 00:11 4.6M
mm39ToGalVar1.over.chain.gz 2020-11-24 01:11 71M
mm39ToGorGor6.over.chain.gz 2020-11-24 04:45 67M
mm39ToHg38.over.chain.gz 2020-08-18 09:09 68M
mm39ToLoxAfr3.over.chain.gz 2020-11-24 23:39 51M
mm39ToManPen1.over.chain.gz 2020-11-23 23:48 56M
mm39ToMm9.over.chain.gz 2022-10-25 14:53 206K
mm39ToMm10.over.chain.gz 2020-07-30 14:54 50K
mm39ToMonDom5.over.chain.gz 2020-11-25 02:08 10M
mm39ToNeoSch1.over.chain.gz 2020-11-24 21:46 62M
mm39ToOchPri3.over.chain.gz 2020-11-25 19:04 38M
mm39ToOryCun2.over.chain.gz 2020-11-24 22:11 50M
mm39ToOtoGar3.over.chain.gz 2020-11-24 13:36 59M
mm39ToOviAri1.over.chain.gz 2021-12-09 17:37 32M
mm39ToOviAri4.over.chain.gz 2020-11-24 22:19 53M
mm39ToPanPan3.over.chain.gz 2020-11-24 05:02 67M
mm39ToPanTro6.over.chain.gz 2020-11-24 04:42 67M
mm39ToPetMar3.over.chain.gz 2020-11-24 23:02 2.2M
mm39ToRheMac10.over.chain.gz 2020-10-20 16:43 67M
mm39ToRn6.over.chain.gz 2020-10-20 16:42 74M
mm39ToRn7.over.chain.gz 2021-02-04 18:08 73M
mm39ToSorAra2.over.chain.gz 2020-11-25 20:18 28M
mm39ToSpeTri2.over.chain.gz 2020-11-25 20:27 67M
mm39ToSusScr3.over.chain.gz 2020-11-24 13:35 52M
mm39ToSusScr11.over.chain.gz 2021-09-24 13:18 55M
mm39ToTarSyr2.over.chain.gz 2020-11-23 18:36 64M
mm39ToTupBel1.over.chain.gz 2020-11-25 21:31 44M
mm39ToTurTru2.over.chain.gz 2020-11-24 13:35 61M
mm39ToXenTro9.over.chain.gz 2020-11-25 01:14 3.7M
mm39ToXenTro10.over.chain.gz 2021-02-23 01:56 3.8M