This directory contains a dump of the UCSC genome annotation database for
the Dec. 2008 assembly of the zebrafish genome (danRer6, Wellcome Trust Sanger Institute, Zv8 assembly (CAAK00000000.5)).
The annotations were generated by UCSC and collaborators worldwide.
This assembly was produced by a collaboration between the
Wellcome Trust Sanger Institute in Cambridge, UK, the Max Planck Institute
for Developmental Biology in Tuebingen, Germany, the Netherlands Institute
for Developmental Biology (Hubrecht Laboratory), Utrecht, The Netherlands
and Yi Zhou and Leonard Zon from the Children's Hospital in Boston,
Massachusetts..
For more information on the zebrafish genome, see the project website:
http://www.sanger.ac.uk/Projects/D_rerio/
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=danRer6
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/danRer6/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/danRer6/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/danRer6/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/danRer6/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/danRer6/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 danRer6 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql danRer6 --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.
Name Last modified Size Description
Parent Directory -
chromInfo.sql 2010-01-06 13:21 1.3K
chromInfo.txt.gz 2010-01-06 13:21 60K
rmsk.sql 2010-01-06 13:21 2.0K
rmsk.txt.gz 2010-01-06 13:21 99M
netOryLat2.sql 2010-01-06 13:22 2.0K
netOryLat2.txt.gz 2010-01-06 13:22 15M
chainSelf.sql 2010-01-06 13:22 1.8K
chainSelf.txt.gz 2010-01-06 13:24 824M
chainOryLat2Link.sql 2010-01-06 13:29 1.5K
chainOryLat2Link.txt.gz 2010-01-06 13:30 302M
nestedRepeats.sql 2010-01-06 13:31 2.0K
nestedRepeats.txt.gz 2010-01-06 13:31 8.5M
gap.sql 2010-01-06 13:32 1.6K
gap.txt.gz 2010-01-06 13:32 584K
simpleRepeat.sql 2010-01-06 13:32 2.0K
simpleRepeat.txt.gz 2010-01-06 13:32 27M
cpgIslandExt.sql 2010-01-06 13:32 1.8K
cpgIslandExt.txt.gz 2010-01-06 13:32 281K
chainHg19Link.sql 2010-01-06 13:32 1.5K
chainHg19Link.txt.gz 2010-01-06 13:34 1.0G
blastHg18KG.sql 2010-01-06 13:41 2.3K
blastHg18KG.txt.gz 2010-01-06 13:41 2.8M
chainHg19.sql 2010-01-06 13:41 1.8K
chainHg19.txt.gz 2010-01-06 13:41 338M
netHg19.sql 2010-01-06 13:43 2.3K
netHg19.txt.gz 2010-01-06 13:43 9.8M
gold.sql 2010-01-06 13:43 1.7K
gold.txt.gz 2010-01-06 13:43 1.2M
gc5Base.sql 2010-01-06 13:43 1.9K
gc5Base.txt.gz 2010-01-06 13:43 6.1M
chainSelfLink.sql 2010-01-06 13:43 1.5K
chainSelfLink.txt.gz 2010-01-06 13:45 1.0G
chainOryLat2.sql 2010-01-06 13:50 1.6K
chainOryLat2.txt.gz 2010-01-06 13:50 69M
chainMm9Link.sql 2010-03-14 10:07 1.5K
chainMm9Link.txt.gz 2010-03-14 10:07 236M
chainGasAcu1.sql 2010-03-14 10:09 1.6K
chainGasAcu1.txt.gz 2010-03-14 10:09 93M
netMm9.sql 2010-03-14 10:09 2.0K
netMm9.txt.gz 2010-03-14 10:09 8.7M
netXenTro2.sql 2010-03-14 10:09 2.0K
netXenTro2.txt.gz 2010-03-14 10:09 11M
chainTetNig2.sql 2010-03-14 10:09 1.6K
chainTetNig2.txt.gz 2010-03-14 10:09 22M
chainMm9.sql 2010-03-14 10:09 1.6K
chainMm9.txt.gz 2010-03-14 10:10 55M
chainXenTro2.sql 2010-03-14 10:10 1.6K
chainXenTro2.txt.gz 2010-03-14 10:10 235M
chainGasAcu1Link.sql 2010-03-14 10:11 1.5K
chainGasAcu1Link.txt.gz 2010-03-14 10:12 424M
chainTetNig2Link.sql 2010-03-14 10:14 1.5K
chainTetNig2Link.txt.gz 2010-03-14 10:14 88M
netGasAcu1.sql 2010-03-14 10:15 2.0K
netGasAcu1.txt.gz 2010-03-14 10:15 16M
chainXenTro2Link.sql 2010-03-14 10:15 1.5K
chainXenTro2Link.txt.gz 2010-03-14 10:16 705M
netTetNig2.sql 2010-03-14 10:19 2.0K
netTetNig2.txt.gz 2010-03-14 10:20 10M
history.sql 2010-07-04 15:07 1.6K
history.txt.gz 2010-07-04 15:07 690
phastCons6way.sql 2010-07-18 13:27 1.7K
phastCons6way.txt.gz 2010-07-18 13:27 16M
multiz6way.sql 2010-07-18 13:27 1.5K
multiz6way.txt.gz 2010-07-18 13:27 34M
phastConsElements6way.sql 2010-07-18 13:27 1.5K
phastConsElements6way.txt.gz 2010-07-18 13:28 8.8M
multiz6wayFrames.sql 2010-07-18 13:28 1.7K
multiz6wayFrames.txt.gz 2010-07-18 13:28 18M
extFile.sql 2010-07-18 13:28 1.4K
extFile.txt.gz 2010-07-18 13:28 80
multiz6waySummary.sql 2010-07-18 13:28 1.5K
multiz6waySummary.txt.gz 2010-07-18 13:28 9.5M
ensGtp.sql 2010-08-29 10:49 1.4K
ensGtp.txt.gz 2010-08-29 10:49 345K
ensPep.sql 2010-08-29 10:49 1.3K
ensPep.txt.gz 2010-08-29 10:49 7.4M
ensGene.sql 2010-08-29 10:50 1.9K
ensGene.txt.gz 2010-08-29 10:50 2.6M
tRNAs.sql 2012-04-22 21:18 1.7K
tRNAs.txt.gz 2012-04-22 21:18 251K
pubsBlat.sql 2012-05-07 14:33 1.9K
pubsBlat.txt.gz 2012-05-07 14:33 440K
pubsBlatPsl.sql 2012-05-07 14:33 2.1K
pubsBlatPsl.txt.gz 2012-05-07 14:33 624K
grp.sql 2014-03-02 03:40 1.4K
grp.txt.gz 2014-03-02 03:40 209
cpgIslandExtUnmasked.sql 2014-06-01 10:52 1.7K
cpgIslandExtUnmasked.txt.gz 2014-06-01 10:52 1.0M
augustusGene.sql 2015-07-26 11:52 1.9K
augustusGene.txt.gz 2015-07-26 11:52 3.0M
microsat.sql 2015-08-23 13:25 1.5K
microsat.txt.gz 2015-08-23 13:25 1.1M
intronEst.sql 2017-11-26 06:44 2.1K
intronEst.txt.gz 2017-11-26 06:44 55M
estOrientInfo.sql 2017-11-26 06:46 1.8K
estOrientInfo.txt.gz 2017-11-26 06:46 21M
all_est.sql 2017-11-26 06:46 2.1K
all_est.txt.gz 2017-11-26 06:46 88M
mgcFullMrna.sql 2020-03-01 05:37 2.1K
mgcFullMrna.txt.gz 2020-03-01 05:37 1.6M
mgcGenes.sql 2020-03-01 05:39 1.9K
mgcGenes.txt.gz 2020-03-01 05:39 1.2M
all_mrna.sql 2020-08-21 08:16 2.1K
all_mrna.txt.gz 2020-08-21 08:16 2.7M
xenoMrna.sql 2020-08-21 08:16 2.1K
xenoMrna.txt.gz 2020-08-21 08:16 262M
refGene.sql 2020-08-21 08:31 1.9K
refGene.txt.gz 2020-08-21 08:31 1.7M
refFlat.sql 2020-08-21 08:31 1.7K
refFlat.txt.gz 2020-08-21 08:31 1.5M
xenoRefGene.sql 2020-08-21 08:31 2.0K
xenoRefGene.txt.gz 2020-08-21 08:31 26M
xenoRefFlat.sql 2020-08-21 08:31 1.7K
xenoRefFlat.txt.gz 2020-08-21 08:31 24M
mrnaOrientInfo.sql 2020-08-21 08:34 1.8K
mrnaOrientInfo.txt.gz 2020-08-21 08:34 845K
refSeqAli.sql 2020-08-21 08:34 2.1K
refSeqAli.txt.gz 2020-08-21 08:34 1.7M
xenoRefSeqAli.sql 2020-08-21 08:34 2.1K
xenoRefSeqAli.txt.gz 2020-08-21 08:34 25M
gbLoaded.sql 2020-08-21 08:47 1.6K
gbLoaded.txt.gz 2020-08-21 08:47 91K
trackDb.sql 2023-03-28 13:48 2.1K
trackDb.txt.gz 2023-03-28 13:48 42K
hgFindSpec.sql 2023-03-28 13:48 1.8K
hgFindSpec.txt.gz 2023-03-28 13:48 959
tableDescriptions.sql 2024-12-07 02:03 1.5K
tableDescriptions.txt.gz 2024-12-07 02:03 7.2K
tableList.sql 2024-12-08 03:06 1.6K
tableList.txt.gz 2024-12-08 03:06 4.2K
bigFiles.sql 2024-12-08 03:06 1.4K
bigFiles.txt.gz 2024-12-08 03:06 33