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 - 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 2024-07-20 02:03 1.4K tableDescriptions.txt.gz 2024-07-20 02:03 7.2K tableList.sql 2024-07-21 03:06 1.6K tableList.txt.gz 2024-07-21 03:06 4.2K bigFiles.sql 2024-07-21 03:06 1.4K bigFiles.txt.gz 2024-07-21 03:06 33