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 2022-03-21 20:13 3.1K 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_013030995.1.over.chain.gz 2022-03-21 20:05 4.9M mm39ToGCF_001704415.1.over.chain.gz 2021-12-09 19:25 53M mm39ToGCF_002742125.1.over.chain.gz 2021-12-21 20:50 52M 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 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