This directory contains the Oct. 2010 (WS220/ce10) assembly of the
C. elegans genome (ce10, Washington University School of Medicine
GSC and Sanger Institute WS220), as well as repeat annotations and
GenBank sequences.

This assembly was produced by the Genome Sequencing Center at the
Washington University in St. Louis (WUSTL) School of Medicine and
the Sanger Institute. For more information on the
C. elegans genome, see the WUSTL project website at
http://genome.wustl.edu/genome.cgi?GENOME=Caenorhabditis+elegans.
and WormBase information:
http://wiki.wormbase.org/index.php/Caenorhabditis_elegans

This UCSC sequence data was downloaded from:
ftp://ftp.sanger.ac.uk/pub/wormbase/WS220/genomes/c_elegans/

Files included in this directory:

ce10.2bit - contains the complete C. elegans/ce10 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 RepeatMasker 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.
    RepeatMasker version:
       June 30 2010 (open-3-2-9) version of RepeatMasker
       CC   RELEASE 20090604

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 5+
    format (one file per chromosome).

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

refMrna.fa.gz - RefSeq mRNA from the same species as the genome.
    This sequence data is updated once a week via automatic GenBank
    updates.

upstream1000.fa.gz - Sequences 1000 bases upstream of annotated
    transcription starts of RefSeq genes with annotated 5' UTRs.
    This file is updated weekly so it might be slightly out of sync with
    the RefSeq data which is updated daily for most assemblies.

upstream2000.fa.gz - Same as upstream1000, but 2000 bases.

upstream5000.fa.gz - Same as upstream1000, but 5000 bases.

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.


ce10.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/ce10/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/ce10/bigZips/ .
For a single file, e.g. chromFa.tar.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/ce10/bigZips/chromFa.tar.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/ce10/bigZips/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/ce10/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. elegans 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 4.9K 
[   ]ce10.2bit23-May-2011 13:23 25M 
[   ]ce10.chrom.sizes23-May-2011 11:38 99  
[   ]chromAgp.tar.gz09-Jun-2011 16:24 55K 
[   ]chromFa.tar.gz09-Jun-2011 16:24 30M 
[   ]chromFaMasked.tar.gz09-Jun-2011 16:25 26M 
[   ]chromOut.tar.gz09-Jun-2011 16:24 2.7M 
[   ]chromTrf.tar.gz09-Jun-2011 16:25 190K 
[TXT]md5sum.txt09-Jun-2011 16:26 457  
[   ]upstream1000.fa.gz09-Jun-2011 16:25 2.7M 
[   ]upstream2000.fa.gz09-Jun-2011 16:25 5.1M 
[   ]upstream5000.fa.gz09-Jun-2011 16:26 12M 

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