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/bosTau6/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/bosTau6/liftOver/ .
For a single file, e.g. bosTau6ToHg19.over.chain.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/bosTau6/liftOver/bosTau6ToHg19.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/bosTau6/liftOver/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/bosTau6/liftOver/bosTau6ToHg19.over.chain.gz'  
        -O bosTau6ToHg19.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                                    -   
      bosTau6ToBosTau4.over.chain.gz 12-May-2012 16:28  7.8M  
      bosTau6ToBosTau5.over.chain.gz 12-May-2012 16:27  7.8M  
      bosTau6ToBosTau7.over.chain.gz 12-May-2012 16:33  7.3M  
      bosTau6ToBosTau8.over.chain.gz 20-Oct-2014 12:18   86K  
      bosTau6ToCanFam2.over.chain.gz 26-May-2011 09:02   83M  
      bosTau6ToCanFam3.over.chain.gz 27-Jun-2012 22:57   82M  
      bosTau6ToEquCab2.over.chain.gz 28-Oct-2014 14:03   73M  
      bosTau6ToHg19.over.chain.gz    23-May-2011 15:25   80M  
      bosTau6ToMm9.over.chain.gz     23-May-2011 15:16   52M  
      bosTau6ToMonDom5.over.chain.gz 01-Jun-2011 10:40   15M  
      bosTau6ToOrnAna1.over.chain.gz 20-May-2011 18:50   16M  
      bosTau6ToRn4.over.chain.gz     31-May-2011 18:36   49M  
      bosTau6ToSusScr2.over.chain.gz 25-May-2011 21:28   70M  
      md5sum.txt                     05-Jan-2015 15:38  896