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.

[ICO]NameLast modifiedSizeDescription

[DIR]Parent Directory  -  
[TXT]README.txt31-Mar-2010 14:29 2.3K 
[   ]calJac3ToCanFam2.over.chain.gz14-Feb-2010 15:57 86M 
[   ]calJac3ToGorGor2.over.chain.gz23-Feb-2010 19:20 62M 
[   ]calJac3ToGorGor3.over.chain.gz26-Oct-2011 09:07 49M 
[   ]calJac3ToHg18.over.chain.gz10-Jan-2011 15:28 51M 
[   ]calJac3ToHg19.over.chain.gz11-Feb-2010 15:49 51M 
[   ]calJac3ToHg38.over.chain.gz13-Dec-2014 19:53 56M 
[   ]calJac3ToMicMur1.over.chain.gz21-Feb-2010 22:16 72M 
[   ]calJac3ToMm9.over.chain.gz14-Feb-2010 15:56 64M 
[   ]calJac3ToMm10.over.chain.gz10-Mar-2012 08:51 64M 
[   ]calJac3ToMonDom5.over.chain.gz14-Feb-2010 16:00 16M 
[   ]calJac3ToOtoGar1.over.chain.gz20-Feb-2010 23:05 76M 
[   ]calJac3ToPanTro2.over.chain.gz11-Feb-2010 15:57 50M 
[   ]calJac3ToPanTro3.over.chain.gz07-Mar-2011 09:54 50M 
[   ]calJac3ToPanTro4.over.chain.gz09-Feb-2015 13:29 56M 
[   ]calJac3ToPanTro5.over.chain.gz08-Aug-2017 18:22 61M 
[   ]calJac3ToPapHam1.over.chain.gz18-Feb-2010 21:30 55M 
[   ]calJac3ToPonAbe2.over.chain.gz12-Feb-2010 10:52 52M 
[   ]calJac3ToRheMac2.over.chain.gz12-Feb-2010 10:51 50M 
[   ]calJac3ToRheMac3.over.chain.gz23-Jul-2012 19:06 51M 
[   ]calJac3ToRheMac8.over.chain.gz08-Aug-2017 17:50 64M 
[   ]calJac3ToSaiBol1.over.chain.gz08-May-2014 11:49 45M 
[   ]calJac3ToTarSyr1.over.chain.gz24-Feb-2010 13:16 78M 
[   ]calJac3ToTarSyr2.over.chain.gz12-Dec-2014 15:53 83M 
[TXT]md5sum.txt08-Aug-2017 19:55 1.4K 

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