This directory contains a dump of the UCSC genome annotation database for
the May 2007 assembly of the C. remanei genome (UCSC version caeRem3, WUSTL 
School of Medicine GSC version 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 (WUSTL).
For more information on the C. remanei genome, see the project website:
http://genome.wustl.edu/genome.cgi?GENOME=Caenorhabditis+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=caeRem3
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/caeRem3/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/caeRem3/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/caeRem3/database/gc5BaseBw.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/caeRem3/database/*'
With wget, a single file: 
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/caeRem3/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 caeRem3 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql caeRem3 --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.cgi for data use
restrictions and citation information.
      Name                      Last modified      Size  Description
Parent Directory - xenoRefSeqAli.txt.gz 2020-08-18 10:36 12M xenoRefSeqAli.sql 2020-08-18 10:36 2.1K xenoRefGene.txt.gz 2020-08-18 10:23 11M xenoRefGene.sql 2020-08-18 10:23 2.0K xenoRefFlat.txt.gz 2020-08-18 10:23 9.3M xenoRefFlat.sql 2020-08-18 10:23 1.7K xenoMrna.txt.gz 2020-08-18 10:13 90M xenoMrna.sql 2020-08-18 10:13 2.1K windowmaskerSdust.txt.gz 2008-06-20 13:16 9.9M windowmaskerSdust.sql 2008-06-20 13:16 1.4K trackDb.txt.gz 2023-03-28 13:46 23K trackDb.sql 2023-03-28 13:46 2.1K tableList.txt.gz 2024-05-19 03:13 2.2K tableList.sql 2024-05-19 03:13 1.6K tableDescriptions.txt.gz 2024-05-18 02:03 4.6K tableDescriptions.sql 2024-05-18 02:03 1.5K tRNAs.txt.gz 2012-04-15 16:19 22K tRNAs.sql 2012-04-15 16:19 1.7K simpleRepeat.txt.gz 2008-06-20 13:16 1.3M simpleRepeat.sql 2008-06-20 13:16 1.9K quality.txt.gz 2008-06-20 13:16 2.5M quality.sql 2008-06-20 13:16 1.7K netCe6.txt.gz 2008-08-01 03:19 3.6M netCe6.sql 2008-08-01 03:19 2.2K mrnaOrientInfo.txt.gz 2016-06-05 09:12 4.5K mrnaOrientInfo.sql 2016-06-05 09:12 1.8K microsat.txt.gz 2015-08-23 11:07 2.1K microsat.sql 2015-08-23 11:07 1.5K intronEst.txt.gz 2016-06-05 09:11 1.1M intronEst.sql 2016-06-05 09:11 2.1K history.txt.gz 2008-06-20 13:15 439 history.sql 2008-06-20 13:15 1.4K hgFindSpec.txt.gz 2023-03-28 13:46 630 hgFindSpec.sql 2023-03-28 13:46 1.8K grp.txt.gz 2014-03-02 03:40 199 grp.sql 2014-03-02 03:40 1.4K gc5Base.txt.gz 2008-06-20 13:15 636K gc5Base.sql 2008-06-20 13:15 1.7K gbLoaded.txt.gz 2020-08-18 10:38 113K gbLoaded.sql 2020-08-18 10:38 1.6K estOrientInfo.txt.gz 2016-06-05 09:12 259K estOrientInfo.sql 2016-06-05 09:12 1.8K ctgPos2.txt.gz 2008-06-20 13:13 175K ctgPos2.sql 2008-06-20 13:13 1.4K chromInfo.txt.gz 2008-06-20 13:13 70 chromInfo.sql 2008-06-20 13:13 1.2K chrUn_gold.txt.gz 2008-06-20 13:13 65K chrUn_gold.sql 2008-06-20 13:13 1.6K chrUn_gap.txt.gz 2008-06-20 13:13 166K chrUn_gap.sql 2008-06-20 13:13 1.5K chrUn_chainCe6Link.txt.gz 2008-08-01 03:18 20M chrUn_chainCe6Link.sql 2008-08-01 03:17 1.4K chrUn_chainCe6.txt.gz 2008-08-01 03:17 2.8M chrUn_chainCe6.sql 2008-08-01 03:17 1.7K blastCe6SG.txt.gz 2008-08-20 03:16 2.0M blastCe6SG.sql 2008-08-20 03:16 2.1K bigFiles.txt.gz 2024-05-19 03:13 33 bigFiles.sql 2024-05-19 03:13 1.4K augustusGene.txt.gz 2015-07-26 10:46 1.7M augustusGene.sql 2015-07-26 10:46 1.9K all_mrna.txt.gz 2016-06-05 09:11 15K all_mrna.sql 2016-06-05 09:11 2.1K all_est.txt.gz 2016-06-05 09:11 1.3M all_est.sql 2016-06-05 09:11 2.1K