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
mm10ToHg19.over.chain.gz file contains the liftOver data needed to
convert mm10 (Mouse GRCm38) coordinates to hg19 (Human GRCh37).
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/mm10/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/mm10/liftOver/ .
For a single file, e.g. mm10ToHg19.over.chain.gz
rsync -avzP
rsync://hgdownload.soe.ucsc.edu/goldenPath/mm10/liftOver/mm10ToHg19.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/mm10/liftOver/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.soe.ucsc.edu/goldenPath/mm10/liftOver/mm10ToHg19.over.chain.gz'
-O mm10ToHg19.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.
------------------------------------------------------------------
This file last updated: 2012-02-09 - 09 February 2012
------------------------------------------------------------------
Name Last modified Size Description
Parent Directory -
md5sum.txt 2024-03-15 17:38 11K
mm10ToAilMel1.over.chain.gz 2012-03-20 17:04 62M
mm10ToAnoCar2.over.chain.gz 2012-04-03 11:38 6.8M
mm10ToAotNan1.over.chain.gz 2017-09-25 19:32 65M
mm10ToAquChr2.over.chain.gz 2017-03-16 18:37 7.7M
mm10ToBalAcu1.over.chain.gz 2018-06-13 11:37 63M
mm10ToBisBis1.over.chain.gz 2017-03-17 20:24 53M
mm10ToBosTau6.over.chain.gz 2012-06-19 12:57 53M
mm10ToBosTau7.over.chain.gz 2012-03-22 10:45 53M
mm10ToBosTau8.over.chain.gz 2014-10-16 12:15 53M
mm10ToBosTau9.over.chain.gz 2018-11-08 13:29 53M
mm10ToCalJac3.over.chain.gz 2012-03-09 19:02 63M
mm10ToCalJac4.over.chain.gz 2020-09-03 18:32 64M
mm10ToCanFam3.over.chain.gz 2012-03-20 16:40 58M
mm10ToCanFam4.over.chain.gz 2020-04-02 18:15 58M
mm10ToCanFam5.over.chain.gz 2020-07-30 06:22 58M
mm10ToCanFam6.over.chain.gz 2021-05-17 16:49 59M
mm10ToCasCan1.over.chain.gz 2018-03-20 00:44 73M
mm10ToCavApe1.over.chain.gz 2018-01-08 22:23 34M
mm10ToCavPor3.over.chain.gz 2012-03-17 10:59 58M
mm10ToCebCap1.over.chain.gz 2017-10-03 17:09 65M
mm10ToCerAty1.over.chain.gz 2017-09-27 14:19 67M
mm10ToCerSim1.over.chain.gz 2012-10-24 06:10 68M
mm10ToChoHof1.over.chain.gz 2012-03-22 10:16 41M
mm10ToChrPic1.over.chain.gz 2012-03-30 11:59 9.5M
mm10ToChrPic2.over.chain.gz 2017-04-06 13:26 7.8M
mm10ToColAng1.over.chain.gz 2017-02-28 14:52 66M
mm10ToCriGri1.over.chain.gz 2017-05-12 12:10 85M
mm10ToCriGriChoV1.over.chain.gz 2017-04-13 21:12 83M
mm10ToCriGriChoV2.over.chain.gz 2018-01-05 16:22 85M
mm10ToDanRer7.over.chain.gz 2012-04-03 10:51 5.8M
mm10ToDanRer10.over.chain.gz 2015-09-11 16:28 6.3M
mm10ToDanRer11.over.chain.gz 2017-06-12 17:04 3.8M
mm10ToDasNov2.over.chain.gz 2012-03-23 12:02 39M
mm10ToDasNov3.over.chain.gz 2012-04-14 04:58 52M
mm10ToDipOrd1.over.chain.gz 2012-03-16 04:46 43M
mm10ToDipOrd2.over.chain.gz 2018-01-01 18:41 50M
mm10ToEchTel1.over.chain.gz 2012-03-24 14:15 27M
mm10ToEchTel2.over.chain.gz 2013-06-13 05:34 30M
mm10ToEnhLutNer1.over.chain.gz 2020-04-15 23:47 58M
mm10ToEquCab2.over.chain.gz 2012-03-16 16:38 66M
mm10ToEquCab3.over.chain.gz 2018-05-25 19:04 67M
mm10ToEriEur1.over.chain.gz 2012-03-24 13:36 25M
mm10ToEulFla1.over.chain.gz 2017-10-04 17:20 66M
mm10ToEulMac1.over.chain.gz 2017-10-05 11:20 67M
mm10ToFelCat4.over.chain.gz 2012-03-20 18:34 49M
mm10ToFelCat5.over.chain.gz 2012-04-14 03:30 59M
mm10ToFelCat9.over.chain.gz 2018-03-14 15:59 59M
mm10ToFicAlb1.over.chain.gz 2018-01-09 12:30 7.3M
mm10ToFr3.over.chain.gz 2012-04-03 13:13 3.8M
mm10ToFukDam1.over.chain.gz 2018-01-01 19:16 61M
mm10ToGCA_001624185.1.over.chain.gz 2021-09-14 18:34 11M
mm10ToGCA_001624445.1.over.chain.gz 2021-09-14 18:19 19M
mm10ToGCA_001624535.1.over.chain.gz 2022-04-22 08:11 12M
mm10ToGCA_001624675.1.over.chain.gz 2023-02-06 20:34 14M
mm10ToGCA_001624865.1_SPRET_EiJ_v1.over.chain.gz 2021-04-12 18:17 26M
mm10ToGCA_001632575.1.over.chain.gz 2023-02-07 06:06 12M
mm10ToGCF_000349665.1.over.chain.gz 2021-10-20 00:07 84M
mm10ToGCF_002742125.1.over.chain.gz 2021-04-12 16:42 53M
mm10ToGCF_003121395.1.over.chain.gz 2023-06-05 03:58 55M
mm10ToGCF_011764305.1.over.chain.gz 2023-05-29 23:52 59M
mm10ToGCF_016699485.2.over.chain.gz 2023-05-29 17:24 4.8M
mm10ToGCF_016772045.2.over.chain.gz 2024-03-15 17:14 54M
mm10ToGCF_017639785.1.over.chain.gz 2023-03-01 14:30 87M
mm10ToGCF_019923935.1.over.chain.gz 2024-01-03 10:46 55M
mm10ToGCF_028858775.1.over.chain.gz 2023-05-30 06:10 70M
mm10ToGCF_028885655.1.over.chain.gz 2023-05-30 00:39 70M
mm10ToGCF_029281585.1.over.chain.gz 2023-05-30 06:34 70M
mm10ToGCF_900094665.1.over.chain.gz 2021-04-26 16:35 36M
mm10ToGCF_900095145.1.over.chain.gz 2021-09-09 12:40 51M
mm10ToGadMor1.over.chain.gz 2012-04-03 16:50 4.4M
mm10ToGalGal4.over.chain.gz 2012-04-03 10:43 7.1M
mm10ToGalGal5.over.chain.gz 2016-04-20 12:33 7.5M
mm10ToGalGal6.over.chain.gz 2018-10-12 11:02 7.4M
mm10ToGalVar1.over.chain.gz 2016-04-26 14:27 70M
mm10ToGasAcu1.over.chain.gz 2012-04-03 10:36 4.3M
mm10ToGeoFor1.over.chain.gz 2012-07-29 14:49 7.1M
mm10ToGorGor3.over.chain.gz 2012-03-08 23:14 65M
mm10ToGorGor5.over.chain.gz 2017-08-04 11:58 68M
mm10ToHetGla1.over.chain.gz 2012-03-16 02:31 64M
mm10ToHetGla2.over.chain.gz 2012-04-14 22:13 65M
mm10ToHg19.over.chain.gz 2012-03-08 11:57 74M
mm10ToHg38.over.chain.gz 2015-04-10 12:46 67M
mm10ToLatCha1.over.chain.gz 2012-04-03 15:49 5.8M
mm10ToLoxAfr3.over.chain.gz 2012-03-20 15:38 51M
mm10ToMacEug2.over.chain.gz 2012-03-24 11:54 12M
mm10ToMacNem1.over.chain.gz 2017-02-28 14:40 67M
mm10ToManLeu1.over.chain.gz 2017-09-25 11:03 66M
mm10ToManPen1.over.chain.gz 2017-03-16 02:11 56M
mm10ToMelGal1.over.chain.gz 2012-04-03 11:53 7.0M
mm10ToMelGal5.over.chain.gz 2017-01-19 12:24 7.5M
mm10ToMelUnd1.over.chain.gz 2012-03-30 04:25 7.1M
mm10ToMicMur1.over.chain.gz 2012-03-13 22:10 55M
mm10ToMicMur3.over.chain.gz 2017-03-05 02:29 66M
mm10ToMicOch1.over.chain.gz 2014-05-16 20:13 82M
mm10ToMm9.over.chain.gz 2012-04-30 21:52 940K
mm10ToMm39.over.chain.gz 2020-07-30 14:50 24K
mm10ToMonDom5.over.chain.gz 2012-03-30 19:24 20M
mm10ToMyoLuc2.over.chain.gz 2012-03-22 09:03 49M
mm10ToNeoSch1.over.chain.gz 2017-09-25 19:26 62M
mm10ToNomLeu1.over.chain.gz 2012-03-08 22:47 66M
mm10ToNomLeu2.over.chain.gz 2012-04-14 21:16 65M
mm10ToOchPri2.over.chain.gz 2012-03-24 06:12 33M
mm10ToOrcOrc1.over.chain.gz 2017-06-15 13:33 61M
mm10ToOreNil1.over.chain.gz 2012-04-03 10:54 4.2M
mm10ToOreNil2.over.chain.gz 2012-04-11 10:56 4.2M
mm10ToOreNil3.over.chain.gz 2017-07-31 13:58 4.3M
mm10ToOrnAna1.over.chain.gz 2012-03-30 12:18 11M
mm10ToOryCun2.over.chain.gz 2012-03-17 15:22 51M
mm10ToOryLat2.over.chain.gz 2012-04-03 15:15 4.2M
mm10ToOtoGar3.over.chain.gz 2012-03-13 22:13 59M
mm10ToOviAri1.over.chain.gz 2012-03-22 06:52 32M
mm10ToOviAri3.over.chain.gz 2015-01-08 12:26 33M
mm10ToOviAri4.over.chain.gz 2018-04-25 14:01 52M
mm10ToPanPan2.over.chain.gz 2016-05-24 18:07 67M
mm10ToPanPan3.over.chain.gz 2020-06-15 15:55 67M
mm10ToPanTro3.over.chain.gz 2012-03-12 09:06 67M
mm10ToPanTro4.over.chain.gz 2012-03-10 03:36 66M
mm10ToPanTro5.over.chain.gz 2016-08-04 02:48 67M
mm10ToPanTro6.over.chain.gz 2018-03-25 02:38 67M
mm10ToPapAnu3.over.chain.gz 2017-06-22 06:05 66M
mm10ToPapAnu4.over.chain.gz 2018-01-09 02:02 66M
mm10ToPapHam1.over.chain.gz 2012-03-10 03:12 67M
mm10ToPelSin1.over.chain.gz 2016-05-10 13:22 8.6M
mm10ToPetMar1.over.chain.gz 2012-04-03 15:51 2.8M
mm10ToPetMar2.over.chain.gz 2012-10-19 19:12 2.6M
mm10ToPetMar3.over.chain.gz 2018-01-25 11:15 3.4M
mm10ToPonAbe2.over.chain.gz 2012-03-09 08:43 67M
mm10ToPonAbe3.over.chain.gz 2018-03-26 17:33 67M
mm10ToProCap1.over.chain.gz 2012-03-23 15:53 35M
mm10ToProCoq1.over.chain.gz 2017-09-28 21:26 64M
mm10ToPteVam1.over.chain.gz 2012-03-20 15:44 56M
mm10ToRheMac2.over.chain.gz 2014-05-23 17:43 65M
mm10ToRheMac3.over.chain.gz 2012-07-11 04:40 65M
mm10ToRheMac8.over.chain.gz 2016-02-10 12:51 66M
mm10ToRheMac10.over.chain.gz 2019-07-03 16:18 67M
mm10ToRn4.over.chain.gz 2012-03-08 14:22 52M
mm10ToRn5.over.chain.gz 2012-03-26 12:53 64M
mm10ToRn6.over.chain.gz 2016-04-07 16:17 74M
mm10ToRn7.over.chain.gz 2021-02-15 14:38 73M
mm10ToSaiBol1.over.chain.gz 2012-03-09 19:20 63M
mm10ToSarHar1.over.chain.gz 2012-03-30 10:30 18M
mm10ToSorAra1.over.chain.gz 2012-03-24 06:58 23M
mm10ToSorAra2.over.chain.gz 2013-06-13 01:47 28M
mm10ToSpeTri2.over.chain.gz 2012-03-16 05:26 67M
mm10ToSusScr2.over.chain.gz 2012-03-17 12:53 47M
mm10ToSusScr3.over.chain.gz 2012-04-14 04:18 52M
mm10ToSusScr11.over.chain.gz 2017-07-31 17:20 55M
mm10ToTaeGut1.over.chain.gz 2012-04-03 11:04 7.2M
mm10ToTarSyr1.over.chain.gz 2012-03-12 05:15 53M
mm10ToTarSyr2.over.chain.gz 2015-03-27 14:59 64M
mm10ToTetNig2.over.chain.gz 2012-04-02 22:47 3.7M
mm10ToThaSir1.over.chain.gz 2018-03-13 12:17 6.6M
mm10ToTriMan1.over.chain.gz 2012-03-30 12:53 53M
mm10ToTupBel1.over.chain.gz 2012-03-17 20:42 44M
mm10ToTupChi1.over.chain.gz 2017-03-09 16:18 51M
mm10ToTurTru1.over.chain.gz 2012-03-17 16:30 58M
mm10ToTurTru2.over.chain.gz 2012-04-14 21:26 62M
mm10ToVicPac1.over.chain.gz 2012-03-17 20:22 47M
mm10ToVicPac2.over.chain.gz 2013-06-20 19:44 59M
mm10ToXenLae2.over.chain.gz 2017-03-30 09:39 6.3M
mm10ToXenTro3.over.chain.gz 2012-04-03 12:21 6.6M
mm10ToXenTro9.over.chain.gz 2017-03-30 10:16 6.8M
mm10ToXenTro10.over.chain.gz 2021-02-23 02:29 7.6M