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