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.
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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/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;'
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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 -
bigFiles.txt.gz 2024-11-17 03:26 33
chromInfo.txt.gz 2008-06-27 03:19 70
grp.txt.gz 2014-03-02 03:40 199
mrnaOrientInfo.txt.gz 2014-09-07 07:34 255
history.txt.gz 2008-06-27 03:26 464
hgFindSpec.txt.gz 2023-03-28 13:46 631
all_mrna.txt.gz 2014-09-07 07:30 853
chromInfo.sql 2008-06-27 03:19 1.2K
windowmaskerSdust.sql 2008-06-27 03:30 1.4K
grp.sql 2014-03-02 03:40 1.4K
bigFiles.sql 2024-11-17 03:26 1.4K
ctgPos2.sql 2008-06-27 03:19 1.4K
chrUn_chainCe6Link.sql 2008-06-27 03:18 1.4K
history.sql 2008-06-27 03:26 1.4K
tableDescriptions.sql 2024-11-16 02:03 1.5K
microsat.sql 2015-08-23 10:44 1.5K
chrUn_gap.sql 2008-06-27 03:18 1.5K
chrUn_gold.sql 2008-06-27 03:18 1.6K
tableList.sql 2024-11-17 03:26 1.6K
chrUn_chainCe6.sql 2008-06-27 03:17 1.7K
gbLoaded.sql 2020-08-18 09:53 1.7K
tRNAs.sql 2012-04-15 15:52 1.7K
gc5Base.sql 2008-06-27 03:26 1.7K
quality.sql 2008-06-27 03:28 1.7K
hgFindSpec.sql 2023-03-28 13:46 1.8K
xenoRefFlat.sql 2020-08-18 09:40 1.8K
estOrientInfo.sql 2016-06-05 09:09 1.9K
mrnaOrientInfo.sql 2014-09-07 07:34 1.9K
simpleRepeat.sql 2008-06-27 03:29 1.9K
augustusGene.sql 2015-07-26 10:34 1.9K
trackDb.sql 2023-03-28 13:46 2.1K
xenoRefGene.sql 2020-08-18 09:40 2.1K
blastCe6SG.sql 2008-08-20 03:15 2.1K
netCe6.sql 2008-06-27 03:27 2.2K
xenoMrna.sql 2020-08-18 09:35 2.3K
all_est.sql 2016-06-05 09:08 2.3K
all_mrna.sql 2014-09-07 07:30 2.3K
intronEst.sql 2016-06-05 09:08 2.3K
xenoRefSeqAli.sql 2020-08-18 09:40 2.3K
tableList.txt.gz 2024-11-17 03:26 2.4K
microsat.txt.gz 2015-08-23 10:44 3.8K
tableDescriptions.txt.gz 2024-11-16 02:03 4.6K
tRNAs.txt.gz 2012-04-15 15:52 17K
trackDb.txt.gz 2023-03-28 13:46 23K
ctgPos2.txt.gz 2008-06-27 03:19 67K
gbLoaded.txt.gz 2020-08-18 09:53 171K
estOrientInfo.txt.gz 2016-06-05 09:09 355K
chrUn_gap.txt.gz 2008-06-27 03:18 457K
chrUn_gold.txt.gz 2008-06-27 03:18 593K
gc5Base.txt.gz 2008-06-27 03:26 727K
intronEst.txt.gz 2016-06-05 09:08 909K
augustusGene.txt.gz 2015-07-26 10:34 1.0M
all_est.txt.gz 2016-06-05 09:08 1.2M
blastCe6SG.txt.gz 2008-08-20 03:15 1.7M
chrUn_chainCe6.txt.gz 2008-06-27 03:17 2.2M
simpleRepeat.txt.gz 2008-06-27 03:29 2.2M
netCe6.txt.gz 2008-06-27 03:27 2.5M
quality.txt.gz 2008-06-27 03:28 3.0M
xenoRefFlat.txt.gz 2020-08-18 09:40 7.6M
windowmaskerSdust.txt.gz 2008-06-27 03:30 8.3M
xenoRefGene.txt.gz 2020-08-18 09:40 8.8M
xenoRefSeqAli.txt.gz 2020-08-18 09:40 10M
chrUn_chainCe6Link.txt.gz 2008-06-27 03:18 11M
xenoMrna.txt.gz 2020-08-18 09:35 85M