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