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/oryLat2/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/oryLat2/liftOver/ .
For a single file, e.g. oryLat2ToHg18.over.chain.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/oryLat2/liftOver/oryLat2ToHg18.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/oryLat2/liftOver/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/oryLat2/liftOver/oryLat2ToHg18.over.chain.gz'  
        -O oryLat2ToHg18.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.

Checksum values for all files in this directory can be found in md5sum.txt.

      Name                            Last modified      Size  Description
      Parent Directory                                     -   
      md5sum.txt                      10-Feb-2017 07:29  1.1K  
      oryLat2ToDanRer5.over.chain.gz  27-Aug-2008 23:48   13M  
      oryLat2ToDanRer6.over.chain.gz  13-Aug-2009 21:47   11M  
      oryLat2ToDanRer7.over.chain.gz  17-Dec-2010 14:53   12M  
      oryLat2ToDanRer10.over.chain.gz 10-Feb-2017 07:15   11M  
      oryLat2ToFr2.over.chain.gz      26-Aug-2008 10:45   14M  
      oryLat2ToFr3.over.chain.gz      02-Dec-2011 10:17   14M  
      oryLat2ToGasAcu1.over.chain.gz  26-Aug-2008 22:30   16M  
      oryLat2ToHg18.over.chain.gz     25-Aug-2008 13:55  3.7M  
      oryLat2ToMm9.over.chain.gz      27-Aug-2008 13:38  3.6M  
      oryLat2ToMm10.over.chain.gz     04-Apr-2012 13:32  3.6M  
      oryLat2ToPetMar1.over.chain.gz  26-Aug-2008 23:07  4.4M  
      oryLat2ToPetMar2.over.chain.gz  23-Oct-2012 23:45  3.8M  
      oryLat2ToTetNig1.over.chain.gz  27-Aug-2008 11:05   13M  
      oryLat2ToTetNig2.over.chain.gz  15-Sep-2009 11:29   13M