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 2024-07-14 03:09 4.2K tableList.sql 2024-07-14 03:09 1.6K tableDescriptions.txt.gz 2024-07-13 02:03 7.2K tableDescriptions.sql 2024-07-13 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 2024-07-14 03:09 33 bigFiles.sql 2024-07-14 03:09 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