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