This directory contains the Btau_2.0 cow genome assembly (bosTau2, 
Mar. 2005) produced by the Baylor College of Medicine Human Genome 
Sequencing Center.  For more information about these data, see the 
Baylor web page at http://www.hgsc.bcm.tmc.edu/projects/bovine/.

Files included in this directory:

chr*.fa.gz: gzip compressed FASTA sequence of each chromosome.
    Repeats (from RepeatMasker and Tandem Repeat Finder) 
    are in lower case while non-repeating sequence is in upper case.
    RepeatMasker January 12 2005 version with RepBase
    libraries: RepBase Update 9.11, RM database version 20050112

scaffolds.fa.gz: components of Baylor ChrUn artificial chromosome
    treated as separate scaffolds. Treatment is otherwise the same
    as for chr*.fa.gz above.

md5sum.txt - MD5 checksum of these files to verify correct transmission

UCSC modifications made to the original data set:
 - Chr changed to chr
 - Chr30 renamed to chrX
 - ChrUn split into scaffold1 through scaffold98058
 - Bin0 fragments assembled into artificial chromosome chrBin0
    with 500 bp-gap padding
 - chrM obtained from NCBI (gi=12800) 

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If you plan 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, 
then go to the directory goldenPath/bosTau2/chromosomes. To download 
multiple files, use the "mget" command:

    mget <filename1> <filename2> ...
    - or -
    mget -a (to download all the files in the directory)


To unpack the fa.gz files:
    gunzip <file>.fa.gz

Please review the restrictions on the use of the cow assembly data at
http://www.hgsc.bcm.tmc.edu/projects/conditions_for_use.html.
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