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/canFam3/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/canFam3/liftOver/ .
For a single file, e.g. canFam3ToHg19.over.chain.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/canFam3/liftOver/canFam3ToHg19.over.chain.gz .
(Hg19 is merely an example here, not necessarily existing.)
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/canFam3/liftOver/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/canFam3/liftOver/canFam3ToHg19.over.chain.gz'
-O canFam3ToHg19.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 -
canFam3ToAilMel1.over.chain.gz 2014-05-23 13:58 63M
canFam3ToBosTau6.over.chain.gz 2012-06-25 20:55 81M
canFam3ToBosTau7.over.chain.gz 2012-06-24 13:03 81M
canFam3ToCanFam2.over.chain.gz 2012-11-29 15:57 666K
canFam3ToCanFam4.over.chain.gz 2020-05-12 23:02 5.4M
canFam3ToCanFam5.over.chain.gz 2020-07-28 14:46 6.5M
canFam3ToCanFam6.over.chain.gz 2021-05-17 19:09 4.2M
canFam3ToEquCab2.over.chain.gz 2014-05-22 15:57 71M
canFam3ToFelCat8.over.chain.gz 2014-12-11 16:06 70M
canFam3ToGCF_009762305.2.over.chain.gz 2024-06-29 09:28 68M
canFam3ToGCF_014441545.1.over.chain.gz 2022-01-14 07:56 6.5M
canFam3ToGalGal4.over.chain.gz 2015-09-25 18:18 5.1M
canFam3ToHg19.over.chain.gz 2012-07-04 17:20 84M
canFam3ToHg38.over.chain.gz 2015-04-10 12:55 84M
canFam3ToLepWed1.over.chain.gz 2014-05-23 14:21 62M
canFam3ToMm9.over.chain.gz 2015-09-29 10:24 57M
canFam3ToMm10.over.chain.gz 2012-03-21 09:19 57M
canFam3ToMm39.over.chain.gz 2021-09-24 17:16 57M
canFam3ToMusFur1.over.chain.gz 2014-05-22 15:53 68M
canFam3ToMyoLuc2.over.chain.gz 2013-12-22 20:58 60M
canFam3ToOdoRosDiv1.over.chain.gz 2013-12-22 23:43 63M
canFam3ToPanTro4.over.chain.gz 2013-05-02 10:35 83M
canFam3ToPteVam1.over.chain.gz 2014-05-23 13:59 68M
canFam3ToRheMac3.over.chain.gz 2015-09-29 10:03 83M
canFam3ToRn4.over.chain.gz 2015-09-29 09:55 54M
canFam3ToRn5.over.chain.gz 2012-12-04 09:19 56M
canFam3ToRn6.over.chain.gz 2017-01-14 18:11 56M
canFam3ToSorAra2.over.chain.gz 2014-05-05 15:23 53M
canFam3ToTarSyr2.over.chain.gz 2015-04-02 16:06 86M
canFam3ToXenTro9.over.chain.gz 2017-04-06 13:29 3.2M
md5sum.txt 2024-06-29 10:33 1.8K