This directory contains a dump of the UCSC genome annotation database for
the Jul. 2007 (WS220/caeRem4) assembly of the C. remanei genome
(caeRem4, Washington University School of Medicine GSC C. remanei 15.0.1).
The annotations were generated by UCSC and collaborators worldwide.

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. remanei genome, see the project website:
http://genome.wustl.edu/genomes/view/caenorhabditis_remanei/

This UCSC sequence was obtained from:
ftp://ftp.sanger.ac.uk/pub/wormbase/WS220/genomes/c_remanei/

Files included in this directory (updated nightly):

  - *.sql files:  the MySQL commands used to create the tables

  - *.txt.gz files: the database tables in a tab-delimited format
    compressed with gzip.

To see descriptions of the tables underlying Genome Browser annotation
tracks, select the table in the Table Browser:
  http://genome.ucsc.edu/cgi-bin/hgTables?db=caeRem4
and click the "describe table schema" button.  There is also a "view
table schema" link on the configuration page for each track.

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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/caeRem4/database/. 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/caeRem4/database/ .
For a single file, e.g. gc5Base.txt.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/caeRem4/database/gc5Base.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/caeRem4/database/*'
With wget, a single file: 
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/caeRem4/database/gc5Base.txt.gz' 
        -O gc5Base.txt.gz

To uncompress the *.txt.gz files:
    gunzip <table>.txt.gz
The tables can be loaded directly from the .txt.gz compressed file.
It is not necessary to uncompress them to load into a database,
as shown in the example below.

To load one of the tables directly into your local mirror database,
for example the table chromInfo:
## create table from the sql definition
$ hgsql caeRem4 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql caeRem4 --local-infile=1 
        -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'

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The C. remanei 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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