This directory contains the Mar. 2008 assembly of the C. japonica genome
(UCSC version caeJap1, WUSTL School of Medicine GSC version 3.0.2) 
as well as repeat annotations and GenBank sequences.

This assembly was produced by the Genome Sequencing Center at
the Washington University School of Medicine in St. Louis (WUSTL).
For more information on the C. remanei genome, see the project website:
http://genome.wustl.edu/genome.cgi?GENOME=Caenorhabditis+japonica.

Files included in this directory:

caeJap1.2bit - contains the complete C. japonica/caeJap1 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.tar.gz - Description of how the assembly was generated from
    fragments, unpacking to one file per chromosome.

chromFa.tar.gz - The assembly sequence in one file per chromosome.
    Repeats from WindowMasker and Tandem Repeats Finder (with period
    of 12 or less) are shown in lower case; non-repeating sequence is
    shown in upper case.

chromFaMasked.tar.gz - The assembly sequence in one file per chromosome.
    Repeats are masked by capital Ns; non-repeating sequence is shown in
    upper case.

chromOut.tar.gz - RepeatMasker .out files (one file per chromosome).
    RepeatMasker was run with the -s (sensitive) setting.
    Repeat masker version:  Revision 1.213  2008/01/12 01:21:36
    Repeat Libraries version: RELEASE 20071204
    NOTE: the WindowMasker repeat annotations were used to make the
    masked sequence

chromWMSdust.bed.gz - bed file for chrUn used as repeat areas
        identified by WindowMasker with the -sdust option.

chromTrf.tar.gz - Tandem Repeats Finder locations, filtered to keep repeats
    with period less than or equal to 12, and translated into UCSC's BED
    format (one file per chromosome).

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.

caeJap1.chrom.sizes - Two-column tab-separated text file containing assembly
    sequence names and sizes.

------------------------------------------------------------------
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/caeJap1/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/caeJap1/bigZips/ .
For a single file, e.g. chromFa.tar.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/caeJap1/bigZips/chromFa.tar.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/caeJap1/bigZips/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/caeJap1/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

------------------------------------------------------------------
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.cgi for data use
restrictions and citation information.
[ICO]NameLast modifiedSizeDescription

[DIR]Parent Directory  -  
[TXT]README.txt20-Feb-2015 15:32 4.3K 
[   ]caeJap1.2bit03-Apr-2008 22:58 44M 
[   ]caeJap1.chrom.sizes03-Apr-2008 13:48 16  
[   ]chromAgp.tar.gz20-Jun-2008 14:55 901K 
[   ]chromFa.tar.gz20-Jun-2008 14:55 42M 
[   ]chromFaMasked.tar.gz20-Jun-2008 14:56 27M 
[   ]chromOut.tar.gz20-Jun-2008 14:55 1.3M 
[   ]chromTrf.tar.gz20-Jun-2008 14:56 278K 
[TXT]md5sum.txt12-Dec-2013 08:54 355  

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