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/rn6/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/rn6/liftOver/ .
For a single file, e.g. rn6ToHg19.over.chain.gz
    rsync -avzP 
        rsync://hgdownload.soe.ucsc.edu/goldenPath/rn6/liftOver/rn6ToHg19.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/rn6/liftOver/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.soe.ucsc.edu/goldenPath/rn6/liftOver/rn6ToHg19.over.chain.gz' 
        -O rn6ToHg19.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 - rn6ToRn5.over.chain.gz 2014-07-25 12:24 5.0M rn6ToHg38.over.chain.gz 2015-02-17 12:21 70M rn6ToHg19.over.chain.gz 2015-06-08 17:26 70M rn6ToDanRer10.over.chain.gz 2015-09-18 15:41 8.3M rn6ToMm10.over.chain.gz 2016-04-08 10:54 78M rn6ToGalGal5.over.chain.gz 2016-05-03 15:13 8.3M rn6ToXenTro7.over.chain.gz 2017-01-12 17:18 10M rn6ToMonDom5.over.chain.gz 2017-01-13 02:40 21M rn6ToPanTro5.over.chain.gz 2017-01-13 07:54 80M rn6ToCanFam3.over.chain.gz 2017-01-13 22:48 59M rn6ToCavPor3.over.chain.gz 2017-01-13 23:27 59M rn6ToRheMac8.over.chain.gz 2017-01-14 05:18 79M rn6ToAilMel1.over.chain.gz 2017-01-16 15:52 63M rn6ToBosTau8.over.chain.gz 2017-01-16 16:43 54M rn6ToMelGal5.over.chain.gz 2017-01-17 18:36 5.2M rn6ToOryCun2.over.chain.gz 2017-01-17 21:14 52M rn6ToFelCat8.over.chain.gz 2017-01-17 23:05 61M rn6ToCalMil1.over.chain.gz 2017-01-18 19:12 3.8M rn6ToOrnAna2.over.chain.gz 2017-01-18 20:21 16M rn6ToTarSyr2.over.chain.gz 2017-01-18 21:54 79M rn6ToRheMac10.over.chain.gz 2020-10-21 08:51 69M rn6ToMm39.over.chain.gz 2020-10-21 09:03 79M rn6ToRn7.over.chain.gz 2021-02-04 16:05 7.7M rn6ToGCF_000349665.1.over.chain.gz 2021-10-20 00:12 88M md5sum.txt 2021-10-20 01:15 1.5K