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.cse.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.cse.ucsc.edu (user: anonymous),
then cd to goldenPath/calJac3/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/calJac3/liftOver/ .
For a single file, e.g. calJac3ToHg18.over.chain.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/calJac3/liftOver/calJac3ToHg18.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/calJac3/liftOver/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/calJac3/liftOver/calJac3ToHg18.over.chain.gz'
-O calJac3ToHg18.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 -
calJac3ToHg19.over.chain.gz 2010-02-11 15:49 51M
calJac3ToPanTro2.over.chain.gz 2010-02-11 15:57 50M
calJac3ToRheMac2.over.chain.gz 2010-02-12 10:51 50M
calJac3ToPonAbe2.over.chain.gz 2010-02-12 10:52 52M
calJac3ToMm9.over.chain.gz 2010-02-14 15:56 64M
calJac3ToCanFam2.over.chain.gz 2010-02-14 15:57 86M
calJac3ToMonDom5.over.chain.gz 2010-02-14 16:00 16M
calJac3ToPapHam1.over.chain.gz 2010-02-18 21:30 55M
calJac3ToMicMur1.over.chain.gz 2010-02-21 22:16 72M
calJac3ToHg18.over.chain.gz 2011-01-10 15:28 51M
calJac3ToPanTro3.over.chain.gz 2011-03-07 09:54 50M
calJac3ToGorGor3.over.chain.gz 2011-10-26 09:07 49M
calJac3ToMm10.over.chain.gz 2012-03-10 08:51 64M
calJac3ToRheMac3.over.chain.gz 2012-07-23 19:06 51M
calJac3ToTarSyr2.over.chain.gz 2014-12-12 15:53 83M
calJac3ToHg38.over.chain.gz 2014-12-13 19:53 56M
calJac3ToPanTro4.over.chain.gz 2015-02-09 13:29 56M
calJac3ToRheMac8.over.chain.gz 2017-08-08 17:50 64M
calJac3ToPanTro5.over.chain.gz 2017-08-08 18:22 61M
md5sum.txt 2017-08-08 19:55 1.4K
calJac3ToCalJac4.over.chain.gz 2020-09-04 16:04 5.8M