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 -
chainHg19Link.txt.gz 2010-01-06 13:34 1.0G
chainSelfLink.txt.gz 2010-01-06 13:45 1.0G
chainSelf.txt.gz 2010-01-06 13:24 824M
chainXenTro2Link.txt.gz 2010-03-14 10:16 705M
chainGasAcu1Link.txt.gz 2010-03-14 10:12 424M
chainHg19.txt.gz 2010-01-06 13:41 338M
chainOryLat2Link.txt.gz 2010-01-06 13:30 302M
xenoMrna.txt.gz 2020-08-21 08:16 262M
chainMm9Link.txt.gz 2010-03-14 10:07 236M
chainXenTro2.txt.gz 2010-03-14 10:10 235M
rmsk.txt.gz 2010-01-06 13:21 99M
chainGasAcu1.txt.gz 2010-03-14 10:09 93M
all_est.txt.gz 2017-11-26 06:46 88M
chainTetNig2Link.txt.gz 2010-03-14 10:14 88M
chainOryLat2.txt.gz 2010-01-06 13:50 69M
intronEst.txt.gz 2017-11-26 06:44 55M
chainMm9.txt.gz 2010-03-14 10:10 55M
multiz6way.txt.gz 2010-07-18 13:27 34M
simpleRepeat.txt.gz 2010-01-06 13:32 27M
xenoRefGene.txt.gz 2020-08-21 08:31 26M
xenoRefSeqAli.txt.gz 2020-08-21 08:34 25M
xenoRefFlat.txt.gz 2020-08-21 08:31 24M
chainTetNig2.txt.gz 2010-03-14 10:09 22M
estOrientInfo.txt.gz 2017-11-26 06:46 21M
multiz6wayFrames.txt.gz 2010-07-18 13:28 18M
netGasAcu1.txt.gz 2010-03-14 10:15 16M
phastCons6way.txt.gz 2010-07-18 13:27 16M
netOryLat2.txt.gz 2010-01-06 13:22 15M
netXenTro2.txt.gz 2010-03-14 10:09 11M
netTetNig2.txt.gz 2010-03-14 10:20 10M
netHg19.txt.gz 2010-01-06 13:43 9.8M
multiz6waySummary.txt.gz 2010-07-18 13:28 9.5M
phastConsElements6way.txt.gz 2010-07-18 13:28 8.8M
netMm9.txt.gz 2010-03-14 10:09 8.7M
nestedRepeats.txt.gz 2010-01-06 13:31 8.5M
ensPep.txt.gz 2010-08-29 10:49 7.4M
gc5Base.txt.gz 2010-01-06 13:43 6.1M
augustusGene.txt.gz 2015-07-26 11:52 3.0M
blastHg18KG.txt.gz 2010-01-06 13:41 2.8M
all_mrna.txt.gz 2020-08-21 08:16 2.7M
ensGene.txt.gz 2010-08-29 10:50 2.6M
refSeqAli.txt.gz 2020-08-21 08:34 1.7M
refGene.txt.gz 2020-08-21 08:31 1.7M
mgcFullMrna.txt.gz 2020-03-01 05:37 1.6M
refFlat.txt.gz 2020-08-21 08:31 1.5M
mgcGenes.txt.gz 2020-03-01 05:39 1.2M
gold.txt.gz 2010-01-06 13:43 1.2M
microsat.txt.gz 2015-08-23 13:25 1.1M
cpgIslandExtUnmasked.txt.gz 2014-06-01 10:52 1.0M
mrnaOrientInfo.txt.gz 2020-08-21 08:34 845K
pubsBlatPsl.txt.gz 2012-05-07 14:33 624K
gap.txt.gz 2010-01-06 13:32 584K
pubsBlat.txt.gz 2012-05-07 14:33 440K
ensGtp.txt.gz 2010-08-29 10:49 345K
cpgIslandExt.txt.gz 2010-01-06 13:32 281K
tRNAs.txt.gz 2012-04-22 21:18 251K
gbLoaded.txt.gz 2020-08-21 08:47 91K
chromInfo.txt.gz 2010-01-06 13:21 60K
trackDb.txt.gz 2023-03-28 13:48 42K
tableDescriptions.txt.gz 2024-11-16 02:03 7.2K
tableList.txt.gz 2024-11-17 03:16 4.2K
netHg19.sql 2010-01-06 13:43 2.3K
blastHg18KG.sql 2010-01-06 13:41 2.3K
xenoRefSeqAli.sql 2020-08-21 08:34 2.1K
refSeqAli.sql 2020-08-21 08:34 2.1K
xenoMrna.sql 2020-08-21 08:16 2.1K
all_mrna.sql 2020-08-21 08:16 2.1K
mgcFullMrna.sql 2020-03-01 05:37 2.1K
intronEst.sql 2017-11-26 06:44 2.1K
all_est.sql 2017-11-26 06:46 2.1K
pubsBlatPsl.sql 2012-05-07 14:33 2.1K
trackDb.sql 2023-03-28 13:48 2.1K
simpleRepeat.sql 2010-01-06 13:32 2.0K
netXenTro2.sql 2010-03-14 10:09 2.0K
netTetNig2.sql 2010-03-14 10:19 2.0K
netOryLat2.sql 2010-01-06 13:22 2.0K
netGasAcu1.sql 2010-03-14 10:15 2.0K
netMm9.sql 2010-03-14 10:09 2.0K
nestedRepeats.sql 2010-01-06 13:31 2.0K
rmsk.sql 2010-01-06 13:21 2.0K
xenoRefGene.sql 2020-08-21 08:31 2.0K
refGene.sql 2020-08-21 08:31 1.9K
augustusGene.sql 2015-07-26 11:52 1.9K
mgcGenes.sql 2020-03-01 05:39 1.9K
pubsBlat.sql 2012-05-07 14:33 1.9K
gc5Base.sql 2010-01-06 13:43 1.9K
ensGene.sql 2010-08-29 10:50 1.9K
chainSelf.sql 2010-01-06 13:22 1.8K
mrnaOrientInfo.sql 2020-08-21 08:34 1.8K
chainHg19.sql 2010-01-06 13:41 1.8K
estOrientInfo.sql 2017-11-26 06:46 1.8K
hgFindSpec.sql 2023-03-28 13:48 1.8K
cpgIslandExt.sql 2010-01-06 13:32 1.8K
xenoRefFlat.sql 2020-08-21 08:31 1.7K
refFlat.sql 2020-08-21 08:31 1.7K
cpgIslandExtUnmasked.sql 2014-06-01 10:52 1.7K
gold.sql 2010-01-06 13:43 1.7K
phastCons6way.sql 2010-07-18 13:27 1.7K
tRNAs.sql 2012-04-22 21:18 1.7K
multiz6wayFrames.sql 2010-07-18 13:28 1.7K
chainXenTro2.sql 2010-03-14 10:10 1.6K
chainTetNig2.sql 2010-03-14 10:09 1.6K
chainOryLat2.sql 2010-01-06 13:50 1.6K
chainGasAcu1.sql 2010-03-14 10:09 1.6K
chainMm9.sql 2010-03-14 10:09 1.6K
gap.sql 2010-01-06 13:32 1.6K
gbLoaded.sql 2020-08-21 08:47 1.6K
tableList.sql 2024-11-17 03:16 1.6K
history.sql 2010-07-04 15:07 1.6K
chainSelfLink.sql 2010-01-06 13:43 1.5K
chainHg19Link.sql 2010-01-06 13:32 1.5K
multiz6waySummary.sql 2010-07-18 13:28 1.5K
phastConsElements6way.sql 2010-07-18 13:27 1.5K
microsat.sql 2015-08-23 13:25 1.5K
chainXenTro2Link.sql 2010-03-14 10:15 1.5K
chainTetNig2Link.sql 2010-03-14 10:14 1.5K
chainOryLat2Link.sql 2010-01-06 13:29 1.5K
chainGasAcu1Link.sql 2010-03-14 10:11 1.5K
chainMm9Link.sql 2010-03-14 10:07 1.5K
multiz6way.sql 2010-07-18 13:27 1.5K
tableDescriptions.sql 2024-11-16 02:03 1.4K
grp.sql 2014-03-02 03:40 1.4K
bigFiles.sql 2024-11-17 03:16 1.4K
ensGtp.sql 2010-08-29 10:49 1.4K
extFile.sql 2010-07-18 13:28 1.4K
chromInfo.sql 2010-01-06 13:21 1.3K
ensPep.sql 2010-08-29 10:49 1.3K
hgFindSpec.txt.gz 2023-03-28 13:48 959
history.txt.gz 2010-07-04 15:07 690
grp.txt.gz 2014-03-02 03:40 209
extFile.txt.gz 2010-07-18 13:28 80
bigFiles.txt.gz 2024-11-17 03:16 33