This directory contains a dump of the UCSC genome annotation database for
the Oct. 2010 (WS220/ce10) assembly of the C. elegans genome
(ce10, Washington University School of Medicine GSC and Sanger Institute WS220).
The annotations were generated by UCSC and collaborators worldwide.
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 (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=ce10
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/ce10/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/ce10/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/ce10/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/ce10/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/ce10/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 ce10 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql ce10 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
------------------------------------------------------------------------
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.
------------------------------------------------------------------------
Name Last modified Size Description
Parent Directory -
gc5BaseBw.sql 2012-01-05 11:43 1.2K
gc5BaseBw.txt.gz 2012-01-05 11:43 60
multiz7waySummary.sql 2012-01-05 11:43 1.5K
multiz7waySummary.txt.gz 2012-01-05 11:43 1.1M
chrM_intronEst.sql 2012-01-05 11:43 2.0K
chrM_intronEst.txt.gz 2012-01-05 11:43 39
ensGene.sql 2012-01-05 11:43 1.8K
ensGtp.sql 2012-01-05 11:43 1.4K
ensGtp.txt.gz 2012-01-05 11:43 252K
ensGene.txt.gz 2012-01-05 11:43 2.1M
chrM_mrna.sql 2012-01-05 11:43 2.0K
chrM_mrna.txt.gz 2012-01-05 11:43 34
history.sql 2012-01-05 11:44 1.5K
history.txt.gz 2012-01-05 11:44 1.5K
multiz7way.sql 2012-01-05 11:44 1.5K
multiz7way.txt.gz 2012-01-05 11:44 5.5M
phastConsElements7way.sql 2012-01-05 11:44 1.5K
phastConsElements7way.txt.gz 2012-01-05 11:44 3.7M
ensPep.sql 2012-01-05 11:44 1.3K
ensPep.txt.gz 2012-01-05 11:44 5.0M
rmsk.sql 2012-01-05 11:45 1.8K
rmsk.txt.gz 2012-01-05 11:45 2.3M
multiz7wayFrames.sql 2012-01-05 11:45 1.7K
multiz7wayFrames.txt.gz 2012-01-05 11:45 3.7M
ensemblToGeneName.sql 2012-01-05 11:45 1.3K
ensemblToGeneName.txt.gz 2012-01-05 11:45 257K
gold.sql 2012-01-05 11:46 1.6K
gold.txt.gz 2012-01-05 11:46 56K
nestedRepeats.sql 2012-01-05 11:46 1.9K
nestedRepeats.txt.gz 2012-01-05 11:46 93K
extFile.sql 2012-01-05 11:46 1.3K
extFile.txt.gz 2012-01-05 11:46 246
simpleRepeat.sql 2012-01-05 11:46 1.9K
phyloP7way.sql 2012-01-05 11:46 1.7K
simpleRepeat.txt.gz 2012-01-05 11:46 1.2M
phyloP7way.txt.gz 2012-01-05 11:46 2.3M
ensemblSource.sql 2012-01-05 11:46 1.3K
ensemblSource.txt.gz 2012-01-05 11:46 176K
chromInfo.sql 2012-01-05 11:46 1.3K
chromInfo.txt.gz 2012-01-05 11:46 127
gap.sql 2012-01-05 11:48 1.5K
gap.txt.gz 2012-01-05 11:48 28
phastCons7way.sql 2012-01-05 11:48 1.7K
phastCons7way.txt.gz 2012-01-05 11:48 2.3M
blastHg18KG.sql 2012-07-15 08:13 2.1K
blastHg18KG.txt.gz 2012-07-15 08:13 906K
pubsBingBlat.sql 2014-01-26 09:30 2.4K
pubsBingBlat.txt.gz 2014-01-26 09:30 762K
pubsBingBlatPsl.sql 2014-01-26 09:30 2.2K
pubsBingBlatPsl.txt.gz 2014-01-26 09:30 603K
grp.sql 2014-03-02 03:40 1.3K
grp.txt.gz 2014-03-02 03:40 209
augustusGene.sql 2015-07-26 11:22 1.9K
augustusGene.txt.gz 2015-07-26 11:22 1.3M
microsat.sql 2015-08-23 12:08 1.5K
microsat.txt.gz 2015-08-23 12:08 3.0K
all_est.sql 2016-06-05 09:16 2.1K
all_est.txt.gz 2016-06-05 09:16 14M
chrIII_est.sql 2016-06-05 09:17 2.1K
chrIII_est.txt.gz 2016-06-05 09:17 2.4M
chrIII_intronEst.sql 2016-06-05 09:17 2.1K
chrIII_intronEst.txt.gz 2016-06-05 09:17 1.9M
chrII_est.sql 2016-06-05 09:17 2.1K
chrII_est.txt.gz 2016-06-05 09:17 2.6M
estOrientInfo.sql 2016-06-05 09:17 1.8K
estOrientInfo.txt.gz 2016-06-05 09:17 4.1M
chrII_intronEst.sql 2016-06-05 09:17 2.1K
chrII_intronEst.txt.gz 2016-06-05 09:17 2.1M
chrIV_est.sql 2016-06-05 09:17 2.1K
chrIV_est.txt.gz 2016-06-05 09:17 2.3M
chrIV_intronEst.sql 2016-06-05 09:17 2.1K
chrIV_intronEst.txt.gz 2016-06-05 09:17 1.8M
chrI_est.sql 2016-06-05 09:17 2.1K
chrI_est.txt.gz 2016-06-05 09:17 3.0M
chrI_intronEst.sql 2016-06-05 09:17 2.1K
chrI_intronEst.txt.gz 2016-06-05 09:17 2.2M
chrM_est.sql 2016-06-05 09:17 2.1K
chrM_est.txt.gz 2016-06-05 09:17 52K
chrV_est.sql 2016-06-05 09:17 2.1K
chrV_est.txt.gz 2016-06-05 09:17 2.3M
chrV_intronEst.sql 2016-06-05 09:17 2.1K
chrV_intronEst.txt.gz 2016-06-05 09:17 1.8M
chrX_est.sql 2016-06-05 09:17 2.1K
chrX_est.txt.gz 2016-06-05 09:17 1.8M
chrX_intronEst.sql 2016-06-05 09:17 2.1K
chrX_intronEst.txt.gz 2016-06-05 09:17 1.5M
crisprRanges.sql 2016-11-06 06:22 1.4K
crisprRanges.txt.gz 2016-11-06 06:22 322K
crisprTargets.sql 2016-11-06 06:22 1.3K
crisprTargets.txt.gz 2016-11-06 06:22 60
locusName.sql 2016-11-06 06:22 1.5K
locusName.txt.gz 2016-11-06 06:22 2.4M
chrV_mrna.sql 2018-01-07 06:38 2.1K
chrV_mrna.txt.gz 2018-01-07 06:38 41K
chrI_mrna.sql 2020-05-07 16:26 2.1K
chrI_mrna.txt.gz 2020-05-07 16:26 41K
chrII_mrna.sql 2020-08-21 04:40 2.1K
chrII_mrna.txt.gz 2020-08-21 04:40 30K
chrIV_mrna.sql 2020-08-21 04:40 2.1K
chrIV_mrna.txt.gz 2020-08-21 04:40 119K
chrIII_mrna.sql 2020-08-21 04:40 2.1K
chrIII_mrna.txt.gz 2020-08-21 04:40 40K
chrX_mrna.sql 2020-08-21 04:40 2.1K
chrX_mrna.txt.gz 2020-08-21 04:40 47K
all_mrna.sql 2020-08-21 04:40 2.1K
all_mrna.txt.gz 2020-08-21 04:40 318K
xenoMrna.sql 2020-08-21 04:40 2.1K
xenoMrna.txt.gz 2020-08-21 04:40 37M
refGene.sql 2020-08-21 04:52 1.9K
refGene.txt.gz 2020-08-21 04:52 2.3M
refFlat.sql 2020-08-21 05:05 1.7K
refFlat.txt.gz 2020-08-21 05:05 2.1M
xenoRefGene.sql 2020-08-21 05:05 2.0K
xenoRefGene.txt.gz 2020-08-21 05:05 1.7M
xenoRefFlat.sql 2020-08-21 05:07 1.7K
xenoRefFlat.txt.gz 2020-08-21 05:07 1.5M
mrnaOrientInfo.sql 2020-08-21 05:07 1.8K
mrnaOrientInfo.txt.gz 2020-08-21 05:07 845K
refSeqAli.sql 2020-08-21 05:07 2.1K
refSeqAli.txt.gz 2020-08-21 05:07 2.6M
xenoRefSeqAli.sql 2020-08-21 05:07 2.1K
xenoRefSeqAli.txt.gz 2020-08-21 05:07 1.7M
gbLoaded.sql 2020-08-21 05:07 1.6K
gbLoaded.txt.gz 2020-08-21 05:07 95K
trackDb.sql 2023-03-28 13:47 2.1K
trackDb.txt.gz 2023-03-28 13:47 36K
hgFindSpec.sql 2023-03-28 13:47 1.8K
hgFindSpec.txt.gz 2023-03-28 13:47 867
tableDescriptions.sql 2024-11-16 02:03 1.4K
tableDescriptions.txt.gz 2024-11-16 02:03 6.2K
tableList.sql 2024-11-17 03:36 1.6K
tableList.txt.gz 2024-11-17 03:36 4.1K
bigFiles.sql 2024-11-17 03:36 1.4K
bigFiles.txt.gz 2024-11-17 03:36 87