This directory contains v.3.0 draft assembly of the Fugu rubripes 
genome (fr1, Aug. 2002) provided by the US DOE Joint Genome
Institute (JGI). 

Files included in this directory:

fr1.2bit - contains the complete fugu/fr1 genome sequence
    in the 2bit file format.  Repeats from RepeatMasker and Tandem Repeats
    Finder (with period of 12 or less) are shown in lower case; non-repeating
    sequence is shown in upper case.  The utility program, twoBitToFa (available
    from the kent src tree), can be used to extract .fa file(s) from
    this file.  A pre-compiled version of the command line tool can be
    found at:
        http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/
    See also:
        http://genome.ucsc.edu/admin/git.html
	http://genome.ucsc.edu/admin/jk-install.html

chromAgp.zip - Description of how the scaffolds are layed out
    in the unordered "chromosome".

chromFa.zip - The draft sequence as a set of scaffolds in an unordered
    "chromosome", as a single file, chrUn.fa.  Repeats from
    RepeatMasker and Tandem Repeats Finder (with period of 12 or less)
    are in lower case while non-repeating sequence is in upper case.

chromFaMasked.zip - the draft sequence scaffolds, in a single file,
    chrUn.hardmasked.fa, representing the unordered "chromosome".
    Repeats are masked by capital N's; non-repeating sequence 
    is shown in upper case.  

chromOut.zip - RepeatMasker .out file  (chrUn.out), for the single unordered
    "chromosome".  This was created with RepeatMasker at the -s sensitive 
    setting.

chromTrf.zip - Tandem Repeats Finder locations, filtered to keep repeats 
    with period less than or equal to 12, translated into one .bed file 
    for the unordered "chromosome".

contigFa.zip - The draft sequence scaffolds, with multiple scaffolds
    per file, to avoid taxing directory limits.  Repeats from
    RepeatMasker and Tandem Repeats Finder (with period of 12 or less)
    are in lower case while non-repeating sequence is in upper case.

contigFaMasked.zip - the draft sequence scaffolds, with multiple scaffolds
    per file. Repeats are masked by capital N's and
    non-repeating sequence is shown in upper case.  

contigTrf.zip - Tandem Repeats Finder locations, filtered to keep repeats 
    with period less than or equal to 12.  Multiple scaffolds are
    collected into .bed files to avoid overtaxing directory limits.

est.fa.gz - Sequences of all Fugu ESTs in GenBank deposited as of 
    Aug. 2002.

liftAll.zip - A file that contains the offsets of scaffolds within
    the unordered "chromosome" (chrUn).

md5sum.txt - Checksums of files in this directory.

mrna.zip - Fugu mRNA from GenBank.    

xenoMrna.zip - All GenBank mRNA from species other than that of the genome.


fr1.chrom.sizes - Two-column tab-separated text file containing assembly
    sequence names and sizes.

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If you plan to download a large file or multiple files from this 
directory, we recommend 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/fr1/bigZips/. To download multiple files, 
use the "mget" command:

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