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.

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/liftOver.gz .

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.cse.ucsc.edu (user: anonymous),
then cd to goldenPath/hg19/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.cse.ucsc.edu/goldenPath/hg19/liftOver/ .
For a single file, e.g. hg19ToHg18.over.chain.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/hg19/liftOver/hg19ToHg18.over.chain.gz .
    (Hg18 is merely an example here, not necessarily existing.)

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/liftOver/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/liftOver/hg19ToHg18.over.chain.gz'  
        -O hg19ToHg18.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 - hg19ToAilMel1.over.chain.gz 2010-02-04 16:31 78M hg19ToAllMis1.over.chain.gz 2013-06-28 14:03 17M hg19ToAnoCar1.over.chain.gz 2009-05-30 22:56 8.0M hg19ToAnoCar2.over.chain.gz 2011-04-19 13:16 7.8M hg19ToBalAcu1.over.chain.gz 2016-08-19 03:03 80M hg19ToBosTau4.over.chain.gz 2009-06-04 12:27 81M hg19ToBosTau6.over.chain.gz 2011-05-16 20:08 82M hg19ToBosTau7.over.chain.gz 2012-01-23 14:42 81M hg19ToBosTau9.over.chain.gz 2020-12-07 12:55 83M hg19ToCalJac1.over.chain.gz 2009-05-14 12:57 52M hg19ToCalJac3.over.chain.gz 2010-02-11 13:46 50M hg19ToCanFam2.over.chain.gz 2009-05-14 01:08 88M hg19ToCanFam3.over.chain.gz 2012-07-04 02:20 87M hg19ToCavPor3.over.chain.gz 2009-06-04 15:20 83M hg19ToCerSim1.over.chain.gz 2012-10-19 14:06 82M hg19ToChlSab1.over.chain.gz 2013-06-30 11:38 36M hg19ToChoHof1.over.chain.gz 2009-06-05 14:20 67M hg19ToCriGri1.over.chain.gz 2013-09-01 02:51 71M hg19ToDanRer5.over.chain.gz 2009-05-26 19:49 6.4M hg19ToDanRer6.over.chain.gz 2009-07-10 11:40 7.7M hg19ToDanRer7.over.chain.gz 2010-12-18 12:42 6.9M hg19ToDanRer10.over.chain.gz 2015-09-25 08:30 7.2M hg19ToDasNov2.over.chain.gz 2009-05-27 14:12 67M hg19ToDasNov3.over.chain.gz 2013-07-09 13:45 83M hg19ToDipOrd1.over.chain.gz 2009-05-29 19:38 58M hg19ToEchTel1.over.chain.gz 2012-06-29 16:16 54M hg19ToEchTel2.over.chain.gz 2013-06-17 22:34 61M hg19ToEquCab2.over.chain.gz 2009-06-04 13:02 82M hg19ToEriEur1.over.chain.gz 2009-05-30 07:11 46M hg19ToEriEur2.over.chain.gz 2013-07-09 08:24 53M hg19ToFelCat3.over.chain.gz 2009-06-04 15:32 67M hg19ToFelCat4.over.chain.gz 2010-06-08 11:22 75M hg19ToFelCat5.over.chain.gz 2014-02-27 13:53 86M hg19ToFr2.over.chain.gz 2009-05-20 16:19 3.9M hg19ToGalGal3.over.chain.gz 2009-05-14 09:12 7.4M hg19ToGalGal4.over.chain.gz 2013-06-29 23:12 7.5M hg19ToGasAcu1.over.chain.gz 2009-05-14 13:56 4.5M hg19ToGeoFor1.over.chain.gz 2012-07-29 14:41 7.2M hg19ToGorGor1.over.chain.gz 2009-03-22 02:59 27M hg19ToGorGor3.over.chain.gz 2011-10-17 12:44 15M hg19ToGorGor5.over.chain.gz 2017-11-08 14:56 18M hg19ToHg17.over.chain.gz 2012-11-09 15:45 341K hg19ToHg18.over.chain.gz 2009-06-04 15:37 221K hg19ToHg38.over.chain.gz 2013-12-31 23:08 222K hg19ToLoxAfr3.over.chain.gz 2009-07-22 12:24 79M hg19ToMacEug1.over.chain.gz 2009-05-31 04:35 18M hg19ToMacFas5.over.chain.gz 2013-06-30 18:50 35M hg19ToMelGal1.over.chain.gz 2011-03-28 13:01 5.4M hg19ToMicMur1.over.chain.gz 2009-05-22 19:16 71M hg19ToMm9.over.chain.gz 2009-05-13 20:56 75M hg19ToMm10.over.chain.gz 2012-03-07 18:40 75M hg19ToMonDom5.over.chain.gz 2009-05-29 06:34 32M hg19ToMyoLuc1.over.chain.gz 2009-06-04 18:38 63M hg19ToMyoLuc2.over.chain.gz 2013-08-30 01:44 69M hg19ToNomLeu1.over.chain.gz 2011-11-05 01:05 26M hg19ToNomLeu3.over.chain.gz 2013-03-22 16:40 26M hg19ToOchPri2.over.chain.gz 2009-05-30 00:54 59M hg19ToOchPri3.over.chain.gz 2013-06-18 03:01 67M hg19ToOrnAna1.over.chain.gz 2009-05-27 01:17 18M hg19ToOryCun1.over.chain.gz 2009-05-29 06:43 67M hg19ToOryCun2.over.chain.gz 2009-08-12 21:48 78M hg19ToOryLat2.over.chain.gz 2009-05-22 18:25 4.4M hg19ToOtoGar1.over.chain.gz 2009-05-15 02:08 77M hg19ToOviAri1.over.chain.gz 2010-04-16 16:21 57M hg19ToOviAri3.over.chain.gz 2013-06-26 14:32 81M hg19ToPanPan2.over.chain.gz 2018-05-01 22:20 16M hg19ToPanTro2.over.chain.gz 2009-03-19 23:34 13M hg19ToPanTro3.over.chain.gz 2011-02-22 16:33 13M hg19ToPanTro4.over.chain.gz 2013-01-25 14:29 13M hg19ToPanTro5.over.chain.gz 2017-05-04 17:03 13M hg19ToPanTro6.over.chain.gz 2018-12-14 12:15 12M hg19ToPapAnu2.over.chain.gz 2013-08-19 23:49 35M hg19ToPapHam1.over.chain.gz 2009-05-20 17:56 40M hg19ToPetMar1.over.chain.gz 2009-05-14 11:24 3.0M hg19ToPetMar2.over.chain.gz 2012-10-17 12:59 2.8M hg19ToPonAbe2.over.chain.gz 2009-05-14 03:22 26M hg19ToPonAbe3.over.chain.gz 2018-12-14 12:17 23M hg19ToProCap1.over.chain.gz 2009-05-26 12:27 64M hg19ToPteVam1.over.chain.gz 2009-06-04 09:50 75M hg19ToRheMac2.over.chain.gz 2009-05-14 08:53 34M hg19ToRheMac3.over.chain.gz 2012-03-15 19:48 36M hg19ToRheMac8.over.chain.gz 2017-07-06 13:48 37M hg19ToRheMac10.over.chain.gz 2019-07-09 09:57 37M hg19ToRn4.over.chain.gz 2009-05-13 20:44 70M hg19ToRn5.over.chain.gz 2012-06-27 17:52 67M hg19ToRn6.over.chain.gz 2015-06-08 13:42 67M hg19ToSaiBol1.over.chain.gz 2013-06-30 17:42 48M hg19ToSarHar1.over.chain.gz 2013-07-10 13:00 16M hg19ToSorAra1.over.chain.gz 2009-05-29 08:40 46M hg19ToSorAra2.over.chain.gz 2013-06-18 16:24 58M hg19ToSpeTri1.over.chain.gz 2009-06-04 20:15 69M hg19ToSpeTri2.over.chain.gz 2013-08-28 23:27 87M hg19ToSusScr2.over.chain.gz 2010-03-27 02:13 71M hg19ToSusScr3.over.chain.gz 2013-08-29 00:59 79M hg19ToSusScr11.over.chain.gz 2018-04-02 23:15 84M hg19ToTaeGut1.over.chain.gz 2009-05-26 13:04 7.2M hg19ToTaeGut2.over.chain.gz 2013-06-17 23:33 13M hg19ToTarSyr1.over.chain.gz 2009-05-15 16:52 78M hg19ToTetNig1.over.chain.gz 2009-05-14 13:41 4.9M hg19ToTetNig2.over.chain.gz 2009-08-10 14:17 4.0M hg19ToTupBel1.over.chain.gz 2009-06-01 11:22 69M hg19ToTurTru1.over.chain.gz 2009-06-04 13:51 77M hg19ToVicPac1.over.chain.gz 2009-06-04 22:02 67M hg19ToXenTro2.over.chain.gz 2009-05-27 11:15 7.5M hg19ToXenTro3.over.chain.gz 2011-09-20 17:11 7.1M md5sum.txt 2020-07-09 11:59 8.0K