This directory contains the  Sep. 2010 (WUGSC 7.0.1/caeJap3) assembly of
the C. japonica genome (caeJap3, Washington University School of
Medicine GSC C. japonica 7.0.1), as well as repeat annotations and
GenBank sequences.

See also, ABLE03 WGS information:
http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=ABLE03

This assembly was produced by the Genome Sequencing Center at the Washington University School of Medicine in St. Louis.
For more information on the C. japonica genome, see the project website:
http://genome.wustl.edu/genomes/view/caenorhabditis_japonica/

Files included in this directory:

caeJap3.2bit - contains the complete C. japonica/caeJap3 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

caeJap3.agp.gz - Description of how the assembly was generated from
    fragments.

caeJap3.fa.gz - "Soft-masked" assembly sequence in one file.
    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.

caeJap3.fa.masked.gz - "Hard-masked" assembly sequence in one file.
    Repeats are masked by capital Ns; non-repeating sequence is shown in
    upper case.

caeJap3.fa.out.gz - RepeatMasker .out file.  RepeatMasker was run with the
    -s (sensitive) setting.  Repeat Masker version:
    June 30 2010 (open-3-2-9) RELEASE 20090604

caeJap3.trf.bed.gz - Tandem Repeats Finder locations, filtered to keep repeats
    with period less than or equal to 12, and translated into UCSC's BED
    format.

est.fa.gz - C. japonica ESTs in GenBank. This sequence data is updated once a
    week via automatic GenBank updates.

md5sum.txt - checksums of files in this directory

mrna.fa.gz - C. japonica mRNA from GenBank. This sequence data is updated
    once a week via automatic GenBank updates.

xenoMrna.fa.gz - GenBank mRNAs from species other than that of 
    the genome. This sequence data is updated once a week via automatic 
    GenBank updates.

caeJap3.chrom.sizes - Two-column tab-separated text file containing assembly
    sequence names and sizes.

caeJap3.gc5Base.wigVarStep.gz - ascii data wiggle variable step values used
                           - to construct the GC Percent track
caeJap3.gc5Base.wig.gz - wiggle database table for the GC Percent track
                    - this is an older standard alternative to the current
                    - bigWig format of the track, sometimes usefull for analysis
caeJap3.gc5Base.wib    - binary data to correspond with the gc5Base.wig file
    see also:  http://genome.ucsc.edu/goldenPath/help/wiggle.html
    and  http://genomewiki.ucsc.edu/index.php/Using_hgWiggle_without_a_database
         for a discussion of how to use the wig.gz and .wib files for
         interaction with the GC percent data values

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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
[username: anonymous, password: your email address], then cd to the
directory goldenPath/caeJap3/bigZips. To download multiple files, use
the "mget" command:

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

Alternate methods to ftp access.

Using an rsync command to download the entire directory:
    rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/caeJap3/bigZips/ .
For a single file, e.g. chromFa.tar.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/caeJap3/bigZips/chromFa.tar.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/caeJap3/bigZips/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/caeJap3/bigZips/chromFa.tar.gz' 
        -O chromFa.tar.gz

To unpack the *.tar.gz files:
    tar xvzf <file>.tar.gz
To uncompress the fa.gz files:
    gunzip <file>.fa.gz

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The C. japonica sequence is made freely available to the community by the
Genome Sequencing Center at the WUSTL School of Medicine. Please see the
WUSTL data use policy at http://genome.wustl.edu/data/data_use_policy
for data use restrictions and citation information.
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