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/galGal6/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/galGal6/liftOver/ .
For a single file, e.g. galGal6ToHg19.over.chain.gz
rsync -avzP
rsync://hgdownload.soe.ucsc.edu/goldenPath/galGal6/liftOver/galGal6ToHg19.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/galGal6/liftOver/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.soe.ucsc.edu/goldenPath/galGal6/liftOver/galGal6ToHg19.over.chain.gz'
-O galGal6ToHg19.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 -
galGal6ToAmaVit1.over.chain.gz 2018-10-17 17:18 52M
galGal6ToAraMac1.over.chain.gz 2018-10-17 20:33 52M
galGal6ToSerCan1.over.chain.gz 2018-10-21 09:27 51M
galGal6ToColStr1.over.chain.gz 2018-10-18 22:57 51M
galGal6ToZonAlb1.over.chain.gz 2018-10-16 20:28 51M
galGal6ToPseHum1.over.chain.gz 2018-10-21 04:31 51M
galGal6ToFicAlb2.over.chain.gz 2018-10-17 13:45 51M
galGal6ToGeoFor1.over.chain.gz 2018-10-19 18:06 51M
galGal6ToPicPub1.over.chain.gz 2018-10-21 01:52 50M
galGal6ToAcaChl1.over.chain.gz 2018-10-16 23:44 50M
galGal6ToCalAnn1.over.chain.gz 2018-10-18 00:09 50M
galGal6ToMerNub1.over.chain.gz 2018-10-20 10:30 50M
galGal6ToCorBra1.over.chain.gz 2018-10-19 01:04 49M
galGal6ToMelUnd1.over.chain.gz 2018-10-20 10:11 49M
galGal6ToTinGut2.over.chain.gz 2018-10-17 14:34 49M
galGal6ToBucRhi1.over.chain.gz 2018-10-18 00:09 49M
galGal6ToCorCor1.over.chain.gz 2018-10-19 01:45 49M
galGal6ToApaVit1.over.chain.gz 2018-10-17 20:34 48M
galGal6ToMesUni1.over.chain.gz 2018-10-20 11:39 48M
galGal6ToEurHel1.over.chain.gz 2018-10-19 17:45 48M
galGal6ToCucCan1.over.chain.gz 2018-10-19 10:22 48M
galGal6ToCapCar1.over.chain.gz 2018-10-18 00:09 48M
galGal6ToLepDis1.over.chain.gz 2018-10-20 03:39 47M
galGal6ToFalPer1.over.chain.gz 2018-10-19 18:15 47M
galGal6ToFalChe1.over.chain.gz 2018-10-19 18:15 47M
galGal6ToPteGut1.over.chain.gz 2018-10-21 06:48 47M
galGal6ToStrCam1.over.chain.gz 2018-10-21 13:41 47M
galGal6ToChlUnd1.over.chain.gz 2018-10-18 15:24 47M
galGal6ToTauEry1.over.chain.gz 2018-10-21 13:45 47M
galGal6ToColLiv1.over.chain.gz 2018-10-18 17:43 46M
galGal6ToPhaLep1.over.chain.gz 2018-10-20 22:57 46M
galGal6ToTytAlb1.over.chain.gz 2018-10-21 16:03 46M
galGal6ToPhaCar1.over.chain.gz 2018-10-20 22:47 46M
galGal6ToBalPav1.over.chain.gz 2018-10-18 00:03 46M
galGal6ToTaeGut2.over.chain.gz 2018-10-17 11:43 45M
galGal6ToCarCri1.over.chain.gz 2018-10-18 07:33 45M
galGal6ToPelCri1.over.chain.gz 2018-10-20 20:33 45M
galGal6ToEgrGar1.over.chain.gz 2018-10-19 11:21 45M
galGal6ToChaVoc2.over.chain.gz 2018-10-18 09:59 45M
galGal6ToOpiHoa1.over.chain.gz 2018-10-20 18:40 44M
galGal6ToFulGla1.over.chain.gz 2018-10-19 17:42 44M
galGal6ToHalAlb1.over.chain.gz 2018-10-20 01:16 44M
galGal6ToAnaPla1.over.chain.gz 2018-10-17 20:56 44M
galGal6ToGavSte1.over.chain.gz 2018-10-19 17:43 44M
galGal6ToPhoRub1.over.chain.gz 2018-10-21 01:26 44M
galGal6ToNipNip1.over.chain.gz 2018-10-20 18:48 44M
galGal6ToHalLeu1.over.chain.gz 2018-10-20 02:33 44M
galGal6ToAquChr2.over.chain.gz 2018-10-17 17:26 44M
galGal6ToAptFor1.over.chain.gz 2018-10-17 20:41 43M
galGal6ToPygAde1.over.chain.gz 2018-10-21 07:20 42M
galGal6ToChrPic2.over.chain.gz 2018-10-18 16:27 42M
galGal6ToCheMyd1.over.chain.gz 2018-10-18 09:54 42M
galGal6ToGCA_013030995.1.over.chain.gz 2022-03-21 18:44 38M
galGal6ToApaSpi1.over.chain.gz 2018-10-17 20:36 38M
galGal6ToAllSin1.over.chain.gz 2018-10-17 17:18 37M
galGal6ToPelSin1.over.chain.gz 2018-10-20 22:29 37M
galGal6ToAllMis1.over.chain.gz 2018-10-17 09:41 36M
galGal6ToCotJap1.over.chain.gz 2018-10-19 08:12 35M
galGal6ToCotJap2.over.chain.gz 2018-10-26 18:53 28M
galGal6ToMelGal5.over.chain.gz 2018-10-17 10:12 27M
galGal6ToPytBiv1.over.chain.gz 2018-10-21 07:24 15M
galGal6ToAnoCar2.over.chain.gz 2018-10-17 13:11 13M
galGal6ToThaSir1.over.chain.gz 2018-10-21 14:57 12M
galGal6ToHg38.over.chain.gz 2018-10-12 11:10 8.9M
galGal6ToHg19.over.chain.gz 2022-01-12 13:45 8.8M
galGal6ToXenTro9.over.chain.gz 2018-10-17 09:29 7.3M
galGal6ToNanPar1.over.chain.gz 2018-10-20 18:31 7.1M
galGal6ToXenLae2.over.chain.gz 2018-10-21 16:25 7.0M
galGal6ToMm10.over.chain.gz 2018-10-12 11:12 6.4M
galGal6ToDanRer10.over.chain.gz 2020-02-25 11:43 6.0M
galGal6ToDanRer11.over.chain.gz 2018-10-17 11:31 5.9M
galGal6ToAngJap1.over.chain.gz 2018-10-17 00:35 5.4M
galGal6ToOreNil3.over.chain.gz 2018-10-20 19:00 4.5M
galGal6ToTetNig1.over.chain.gz 2018-10-17 07:10 4.4M
galGal6ToGasAcu1.over.chain.gz 2018-10-17 00:18 4.2M
galGal6ToOryLat2.over.chain.gz 2018-10-20 19:42 4.1M
galGal6ToMayZeb1.over.chain.gz 2018-10-20 08:12 4.1M
galGal6ToPetMar3.over.chain.gz 2018-10-17 00:20 3.8M
galGal6ToMm39.over.chain.gz 2020-11-25 01:23 3.8M
galGal6ToTetNig2.over.chain.gz 2018-10-21 12:55 3.6M
galGal6ToLetCam1.over.chain.gz 2018-10-20 07:49 3.5M
galGal6ToGCF_016699485.2.over.chain.gz 2021-10-14 15:04 3.5M
galGal6ToFr3.over.chain.gz 2018-10-17 10:23 3.4M
galGal6ToGalGal5.over.chain.gz 2018-10-11 18:35 1.9M
galGal6ToGalGal4.over.chain.gz 2018-10-12 14:46 1.4M
md5sum.txt 2022-03-21 20:16 5.4K