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/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.soe.ucsc.edu (user: anonymous),
then cd to goldenPath/monDom5/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/monDom5/liftOver/ .
For a single file, e.g. monDom5ToHg18.over.chain.gz
rsync -avzP
rsync://hgdownload.soe.ucsc.edu/goldenPath/monDom5/liftOver/monDom5ToHg18.over.chain.gz .
(Hg18 is merely an example here, not necessarily existing.)
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.soe.ucsc.edu/goldenPath/monDom5/liftOver/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.soe.ucsc.edu/goldenPath/monDom5/liftOver/monDom5ToHg18.over.chain.gz'
-O monDom5ToHg18.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 2017-04-06 21:51 1.9K
monDom5ToPetMar2.over.chain.gz 2012-10-23 21:06 2.1M
monDom5ToMelGal1.over.chain.gz 2011-03-30 18:30 5.6M
monDom5ToXenTro3.over.chain.gz 2011-09-23 08:21 5.7M
monDom5ToXenTro2.over.chain.gz 2008-12-19 19:00 5.7M
monDom5ToXenTro9.over.chain.gz 2017-04-06 21:24 5.7M
monDom5ToMelGal5.over.chain.gz 2017-01-19 20:42 5.9M
monDom5ToDanRer5.over.chain.gz 2008-12-20 16:37 7.2M
monDom5ToGalGal3.over.chain.gz 2008-12-20 16:20 7.5M
monDom5ToMm39.over.chain.gz 2020-11-25 07:42 10M
monDom5ToOviAri1.over.chain.gz 2010-04-16 20:31 10M
monDom5ToRn4.over.chain.gz 2009-06-05 13:07 12M
monDom5ToOryCun2.over.chain.gz 2010-01-25 09:29 13M
monDom5ToSusScr2.over.chain.gz 2010-03-27 08:32 13M
monDom5ToSusScr1.over.chain.gz 2010-01-22 07:03 13M
monDom5ToFelCat4.over.chain.gz 2010-06-12 23:00 14M
monDom5ToBosTau6.over.chain.gz 2011-06-01 09:14 15M
monDom5ToBosTau7.over.chain.gz 2012-01-27 03:09 15M
monDom5ToCalJac3.over.chain.gz 2010-02-14 11:47 16M
monDom5ToAilMel1.over.chain.gz 2010-02-04 23:51 17M
monDom5ToRn5.over.chain.gz 2014-04-02 12:50 19M
monDom5ToRheMac3.over.chain.gz 2012-07-21 01:41 19M
monDom5ToMm10.over.chain.gz 2012-04-02 10:01 20M
monDom5ToMm9.over.chain.gz 2008-12-21 10:11 20M
monDom5ToRn6.over.chain.gz 2017-01-13 08:11 20M
monDom5ToLoxAfr3.over.chain.gz 2011-11-12 02:26 20M
monDom5ToOrnAna1.over.chain.gz 2008-12-20 08:22 21M
monDom5ToCanFam2.over.chain.gz 2008-12-09 03:12 24M
monDom5ToRheMac2.over.chain.gz 2008-12-16 15:48 24M
monDom5ToPonAbe2.over.chain.gz 2008-12-19 01:40 25M
monDom5ToPanTro2.over.chain.gz 2008-12-19 01:42 25M
monDom5ToEquCab2.over.chain.gz 2009-07-01 23:46 26M
monDom5ToHg18.over.chain.gz 2008-12-23 07:21 26M
monDom5ToCerSim1.over.chain.gz 2012-10-29 09:37 27M
monDom5ToBosTau4.over.chain.gz 2008-12-23 10:39 28M
monDom5ToNeoSch1.over.chain.gz 2020-07-17 10:11 30M
monDom5ToPanTro3.over.chain.gz 2011-03-15 12:31 31M
monDom5ToRheMac10.over.chain.gz 2020-07-14 08:08 32M
monDom5ToHg19.over.chain.gz 2009-06-15 10:15 32M
monDom5ToPanTro6.over.chain.gz 2020-07-14 09:08 33M
monDom5ToHg38.over.chain.gz 2014-05-29 15:57 33M
monDom5ToMacEug1.over.chain.gz 2008-12-25 15:57 91M
monDom5ToSarHar1.over.chain.gz 2014-05-01 23:12 109M