This directory contains a dump of the UCSC genome annotation database for
the Mar. 2008 assembly of the C. japonica genome (UCSC version caeJap1, 
WUSTL School of Medicine GSC version 3.0.2). 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 (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 (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=caeJap1
and click the "describe table schema" button.  There is also a "view
table schema" link on the configuration page for each track.

---------------------------------------------------------------
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/caeJap1/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/caeJap1/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/caeJap1/database/gc5BaseBw.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/caeJap1/database/*'
With wget, a single file: 
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/caeJap1/database/gc5BaseBw.txt.gz' 
        -O gc5BaseBw.txt.gz

Please note that some files contents, such as this example gc5BaseBw.txt.gz,
will point to the data being hosted in another /gbdb/ location, which
refers to ftp://hgdownload.cse.ucsc.edu/gbdb/

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 caeJap1 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql caeJap1 --local-infile=1 
        -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'

------------------------------------------------------------------
All the files and tables in this directory are freely usable for any purpose.
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.

      Name                      Last modified      Size  Description
Parent Directory - xenoRefSeqAli.txt.gz 2020-08-18 09:40 10M xenoRefSeqAli.sql 2020-08-18 09:40 2.3K xenoRefGene.txt.gz 2020-08-18 09:40 8.8M xenoRefGene.sql 2020-08-18 09:40 2.1K xenoRefFlat.txt.gz 2020-08-18 09:40 7.6M xenoRefFlat.sql 2020-08-18 09:40 1.8K xenoMrna.txt.gz 2020-08-18 09:35 85M xenoMrna.sql 2020-08-18 09:35 2.3K windowmaskerSdust.txt.gz 2008-06-27 03:30 8.3M windowmaskerSdust.sql 2008-06-27 03:30 1.4K trackDb.txt.gz 2021-12-27 12:21 21K trackDb.sql 2021-12-27 12:21 2.1K tableList.txt.gz 2022-08-07 03:06 2.4K tableList.sql 2022-08-07 03:06 1.6K tableDescriptions.txt.gz 2019-07-21 03:41 4.6K tableDescriptions.sql 2019-07-21 03:41 1.4K tRNAs.txt.gz 2012-04-15 15:52 17K tRNAs.sql 2012-04-15 15:52 1.7K simpleRepeat.txt.gz 2008-06-27 03:29 2.2M simpleRepeat.sql 2008-06-27 03:29 1.9K quality.txt.gz 2008-06-27 03:28 3.0M quality.sql 2008-06-27 03:28 1.7K netCe6.txt.gz 2008-06-27 03:27 2.5M netCe6.sql 2008-06-27 03:27 2.2K mrnaOrientInfo.txt.gz 2014-09-07 07:34 255 mrnaOrientInfo.sql 2014-09-07 07:34 1.9K microsat.txt.gz 2015-08-23 10:44 3.8K microsat.sql 2015-08-23 10:44 1.5K intronEst.txt.gz 2016-06-05 09:08 909K intronEst.sql 2016-06-05 09:08 2.3K history.txt.gz 2008-06-27 03:26 464 history.sql 2008-06-27 03:26 1.4K hgFindSpec.txt.gz 2021-12-27 12:21 582 hgFindSpec.sql 2021-12-27 12:21 1.8K grp.txt.gz 2014-03-02 03:40 199 grp.sql 2014-03-02 03:40 1.4K gc5Base.txt.gz 2008-06-27 03:26 727K gc5Base.sql 2008-06-27 03:26 1.7K gbLoaded.txt.gz 2020-08-18 09:53 171K gbLoaded.sql 2020-08-18 09:53 1.7K estOrientInfo.txt.gz 2016-06-05 09:09 355K estOrientInfo.sql 2016-06-05 09:09 1.9K ctgPos2.txt.gz 2008-06-27 03:19 67K ctgPos2.sql 2008-06-27 03:19 1.4K chromInfo.txt.gz 2008-06-27 03:19 70 chromInfo.sql 2008-06-27 03:19 1.2K chrUn_gold.txt.gz 2008-06-27 03:18 593K chrUn_gold.sql 2008-06-27 03:18 1.6K chrUn_gap.txt.gz 2008-06-27 03:18 457K chrUn_gap.sql 2008-06-27 03:18 1.5K chrUn_chainCe6Link.txt.gz 2008-06-27 03:18 11M chrUn_chainCe6Link.sql 2008-06-27 03:18 1.4K chrUn_chainCe6.txt.gz 2008-06-27 03:17 2.2M chrUn_chainCe6.sql 2008-06-27 03:17 1.7K blastCe6SG.txt.gz 2008-08-20 03:15 1.7M blastCe6SG.sql 2008-08-20 03:15 2.1K bigFiles.txt.gz 2022-08-07 03:06 33 bigFiles.sql 2022-08-07 03:06 1.4K augustusGene.txt.gz 2015-07-26 10:34 1.0M augustusGene.sql 2015-07-26 10:34 1.9K all_mrna.txt.gz 2014-09-07 07:30 853 all_mrna.sql 2014-09-07 07:30 2.3K all_est.txt.gz 2016-06-05 09:08 1.2M all_est.sql 2016-06-05 09:08 2.3K