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 - all_est.sql 2017-11-26 06:46 2.1K all_est.txt.gz 2017-11-26 06:46 88M all_mrna.sql 2020-08-21 08:16 2.1K all_mrna.txt.gz 2020-08-21 08:16 2.7M augustusGene.sql 2015-07-26 11:52 1.9K augustusGene.txt.gz 2015-07-26 11:52 3.0M bigFiles.sql 2021-05-02 03:04 1.4K bigFiles.txt.gz 2021-05-02 03:04 33 blastHg18KG.sql 2010-01-06 13:41 2.3K blastHg18KG.txt.gz 2010-01-06 13:41 2.8M chainGasAcu1.sql 2010-03-14 10:09 1.6K chainGasAcu1.txt.gz 2010-03-14 10:09 93M chainGasAcu1Link.sql 2010-03-14 10:11 1.5K chainGasAcu1Link.txt.gz 2010-03-14 10:12 424M chainHg19.sql 2010-01-06 13:41 1.8K chainHg19.txt.gz 2010-01-06 13:41 338M chainHg19Link.sql 2010-01-06 13:32 1.5K chainHg19Link.txt.gz 2010-01-06 13:34 1.0G chainMm9.sql 2010-03-14 10:09 1.6K chainMm9.txt.gz 2010-03-14 10:10 55M chainMm9Link.sql 2010-03-14 10:07 1.5K chainMm9Link.txt.gz 2010-03-14 10:07 236M chainOryLat2.sql 2010-01-06 13:50 1.6K chainOryLat2.txt.gz 2010-01-06 13:50 69M chainOryLat2Link.sql 2010-01-06 13:29 1.5K chainOryLat2Link.txt.gz 2010-01-06 13:30 302M chainSelf.sql 2010-01-06 13:22 1.8K chainSelf.txt.gz 2010-01-06 13:24 824M chainSelfLink.sql 2010-01-06 13:43 1.5K chainSelfLink.txt.gz 2010-01-06 13:45 1.0G chainTetNig2.sql 2010-03-14 10:09 1.6K chainTetNig2.txt.gz 2010-03-14 10:09 22M chainTetNig2Link.sql 2010-03-14 10:14 1.5K chainTetNig2Link.txt.gz 2010-03-14 10:14 88M chainXenTro2.sql 2010-03-14 10:10 1.6K chainXenTro2.txt.gz 2010-03-14 10:10 235M chainXenTro2Link.sql 2010-03-14 10:15 1.5K chainXenTro2Link.txt.gz 2010-03-14 10:16 705M chromInfo.sql 2010-01-06 13:21 1.3K chromInfo.txt.gz 2010-01-06 13:21 60K cpgIslandExt.sql 2010-01-06 13:32 1.8K cpgIslandExt.txt.gz 2010-01-06 13:32 281K cpgIslandExtUnmasked.sql 2014-06-01 10:52 1.7K cpgIslandExtUnmasked.txt.gz 2014-06-01 10:52 1.0M ensGene.sql 2010-08-29 10:50 1.9K ensGene.txt.gz 2010-08-29 10:50 2.6M 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 estOrientInfo.sql 2017-11-26 06:46 1.8K estOrientInfo.txt.gz 2017-11-26 06:46 21M extFile.sql 2010-07-18 13:28 1.4K extFile.txt.gz 2010-07-18 13:28 80 gap.sql 2010-01-06 13:32 1.6K gap.txt.gz 2010-01-06 13:32 584K gbLoaded.sql 2020-08-21 08:47 1.6K gbLoaded.txt.gz 2020-08-21 08:47 91K gc5Base.sql 2010-01-06 13:43 1.9K gc5Base.txt.gz 2010-01-06 13:43 6.1M gold.sql 2010-01-06 13:43 1.7K gold.txt.gz 2010-01-06 13:43 1.2M grp.sql 2014-03-02 03:40 1.4K grp.txt.gz 2014-03-02 03:40 209 hgFindSpec.sql 2020-10-25 07:52 1.7K hgFindSpec.txt.gz 2020-10-25 07:52 909 history.sql 2010-07-04 15:07 1.6K history.txt.gz 2010-07-04 15:07 690 intronEst.sql 2017-11-26 06:44 2.1K intronEst.txt.gz 2017-11-26 06:44 55M 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 microsat.sql 2015-08-23 13:25 1.5K microsat.txt.gz 2015-08-23 13:25 1.1M mrnaOrientInfo.sql 2020-08-21 08:34 1.8K mrnaOrientInfo.txt.gz 2020-08-21 08:34 845K multiz6way.sql 2010-07-18 13:27 1.5K multiz6way.txt.gz 2010-07-18 13:27 34M multiz6wayFrames.sql 2010-07-18 13:28 1.7K multiz6wayFrames.txt.gz 2010-07-18 13:28 18M multiz6waySummary.sql 2010-07-18 13:28 1.5K multiz6waySummary.txt.gz 2010-07-18 13:28 9.5M nestedRepeats.sql 2010-01-06 13:31 2.0K nestedRepeats.txt.gz 2010-01-06 13:31 8.5M netGasAcu1.sql 2010-03-14 10:15 2.0K netGasAcu1.txt.gz 2010-03-14 10:15 16M netHg19.sql 2010-01-06 13:43 2.3K netHg19.txt.gz 2010-01-06 13:43 9.8M netMm9.sql 2010-03-14 10:09 2.0K netMm9.txt.gz 2010-03-14 10:09 8.7M netOryLat2.sql 2010-01-06 13:22 2.0K netOryLat2.txt.gz 2010-01-06 13:22 15M netTetNig2.sql 2010-03-14 10:19 2.0K netTetNig2.txt.gz 2010-03-14 10:20 10M netXenTro2.sql 2010-03-14 10:09 2.0K netXenTro2.txt.gz 2010-03-14 10:09 11M phastCons6way.sql 2010-07-18 13:27 1.7K phastCons6way.txt.gz 2010-07-18 13:27 16M phastConsElements6way.sql 2010-07-18 13:27 1.5K phastConsElements6way.txt.gz 2010-07-18 13:28 8.8M 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 refFlat.sql 2020-08-21 08:31 1.7K refFlat.txt.gz 2020-08-21 08:31 1.5M refGene.sql 2020-08-21 08:31 1.9K refGene.txt.gz 2020-08-21 08:31 1.7M refSeqAli.sql 2020-08-21 08:34 2.1K refSeqAli.txt.gz 2020-08-21 08:34 1.7M rmsk.sql 2010-01-06 13:21 2.0K rmsk.txt.gz 2010-01-06 13:21 99M simpleRepeat.sql 2010-01-06 13:32 2.0K simpleRepeat.txt.gz 2010-01-06 13:32 27M tRNAs.sql 2012-04-22 21:18 1.7K tRNAs.txt.gz 2012-04-22 21:18 251K tableDescriptions.sql 2019-07-21 03:41 1.4K tableDescriptions.txt.gz 2019-07-21 03:41 7.0K tableList.sql 2021-05-02 03:04 1.6K tableList.txt.gz 2021-05-02 03:04 4.2K trackDb.sql 2020-10-25 07:52 2.0K trackDb.txt.gz 2020-10-25 07:52 41K xenoMrna.sql 2020-08-21 08:16 2.1K xenoMrna.txt.gz 2020-08-21 08:16 262M xenoRefFlat.sql 2020-08-21 08:31 1.7K xenoRefFlat.txt.gz 2020-08-21 08:31 24M xenoRefGene.sql 2020-08-21 08:31 1.9K xenoRefGene.txt.gz 2020-08-21 08:31 26M xenoRefSeqAli.sql 2020-08-21 08:34 2.1K xenoRefSeqAli.txt.gz 2020-08-21 08:34 25M