This directory contains a dump of the UCSC genome annotation database for
the Jul. 2010 (Zv9/danRer7) assembly of the zebrafish genome
(danRer7, Wellcome Trust Sanger Institute Zv9 (GCA_000002035.2)).
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=danRer7
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/danRer7/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/danRer7/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/danRer7/database/gc5BaseBw.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/danRer7/database/*'
With wget, a single file: 
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/danRer7/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 danRer7 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql danRer7 --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 - UMassInput.sql 2011-11-06 09:58 1.7K UMassInput.txt.gz 2011-11-06 09:58 2.2M UMassME1.sql 2011-11-06 09:51 1.7K UMassME1.txt.gz 2011-11-06 09:51 2.4M UMassME1Hotspot.sql 2011-11-06 09:51 1.5K UMassME1Hotspot.txt.gz 2011-11-06 09:51 849K UMassME1Peak.sql 2011-11-06 09:51 1.7K UMassME1Peak.txt.gz 2011-11-06 09:51 1.1M UMassME3.sql 2011-11-06 09:58 1.7K UMassME3.txt.gz 2011-11-06 09:58 1.1M UMassME3Hotspot.sql 2011-11-06 09:51 1.5K UMassME3Hotspot.txt.gz 2011-11-06 09:51 389K UMassME3Peak.sql 2011-11-06 09:58 1.7K UMassME3Peak.txt.gz 2011-11-06 09:58 528K all_est.sql 2017-11-26 06:48 2.1K all_est.txt.gz 2017-11-26 06:48 83M all_mrna.sql 2020-08-21 07:48 2.1K all_mrna.txt.gz 2020-08-21 07:48 2.6M augustusGene.sql 2015-07-26 11:52 1.9K augustusGene.txt.gz 2015-07-26 11:52 2.8M bigFiles.sql 2021-05-02 03:11 1.4K bigFiles.txt.gz 2021-05-02 03:11 114 blastHg18KG.sql 2011-01-19 11:16 2.1K blastHg18KG.txt.gz 2011-01-19 11:16 3.1M chainFr3.sql 2012-06-24 06:38 1.6K chainFr3.txt.gz 2012-06-24 06:38 29M chainFr3Link.sql 2012-06-24 06:38 1.5K chainFr3Link.txt.gz 2012-06-24 06:39 115M chainGasAcu1.sql 2011-03-07 07:34 1.6K chainGasAcu1.txt.gz 2011-03-07 07:35 113M chainGasAcu1Link.sql 2011-03-07 08:03 1.5K chainGasAcu1Link.txt.gz 2011-03-07 08:05 418M chainHg19.sql 2011-03-07 07:21 1.6K chainHg19.txt.gz 2011-03-07 07:23 317M chainHg19Link.sql 2011-03-07 07:00 1.5K chainHg19Link.txt.gz 2011-03-07 07:05 1.0G chainMelGal1.sql 2011-11-06 09:51 1.6K chainMelGal1.txt.gz 2011-11-06 09:51 5.3M chainMelGal1Link.sql 2011-11-06 09:51 1.5K chainMelGal1Link.txt.gz 2011-11-06 09:51 19M chainMm10.sql 2013-10-27 12:05 1.7K chainMm10.txt.gz 2013-10-27 12:05 53M chainMm10Link.sql 2013-10-27 12:05 1.5K chainMm10Link.txt.gz 2013-10-27 12:05 234M chainOryLat2.sql 2011-03-07 08:11 1.6K chainOryLat2.txt.gz 2011-03-07 08:12 76M chainOryLat2Link.sql 2011-03-07 07:56 1.5K chainOryLat2Link.txt.gz 2011-03-07 07:57 313M chainPanTro3.sql 2011-03-14 11:24 1.6K chainPanTro3.txt.gz 2011-03-14 11:25 161M chainPanTro3Link.sql 2011-03-14 11:10 1.5K chainPanTro3Link.txt.gz 2011-03-14 11:15 535M chainTetNig2.sql 2011-03-07 06:59 1.6K chainTetNig2.txt.gz 2011-03-07 06:59 25M chainTetNig2Link.sql 2011-03-07 07:19 1.5K chainTetNig2Link.txt.gz 2011-03-07 07:19 92M chainXenTro3.sql 2011-11-06 09:57 1.6K chainXenTro3.txt.gz 2011-11-06 09:57 222M chainXenTro3Link.sql 2011-11-06 09:51 1.5K chainXenTro3Link.txt.gz 2011-11-06 09:53 687M chromAlias.sql 2018-02-18 06:10 1.4K chromAlias.txt.gz 2018-02-18 06:10 5.7K chromInfo.sql 2011-01-19 10:55 1.3K chromInfo.txt.gz 2011-01-19 10:55 7.3K cpgIslandExt.sql 2011-08-07 08:02 1.6K cpgIslandExt.txt.gz 2011-08-07 08:02 271K cpgIslandExtUnmasked.sql 2014-06-01 10:57 1.7K cpgIslandExtUnmasked.txt.gz 2014-06-01 10:57 1.0M crisprRanges.sql 2016-11-06 06:40 1.4K crisprRanges.txt.gz 2016-11-06 06:40 1.4M crisprTargets.sql 2016-11-06 06:40 1.3K crisprTargets.txt.gz 2016-11-06 06:40 63 ctgPos2.sql 2011-01-19 11:12 1.5K ctgPos2.txt.gz 2011-01-19 11:12 13K cytoBandIdeo.sql 2013-04-28 12:53 1.5K cytoBandIdeo.txt.gz 2013-04-28 12:53 6.4K ensGene.sql 2014-04-06 15:50 1.9K ensGene.txt.gz 2014-04-06 15:50 3.7M ensGtp.sql 2014-04-06 15:46 1.4K ensGtp.txt.gz 2014-04-06 15:46 540K ensPep.sql 2014-04-06 15:46 1.3K ensPep.txt.gz 2014-04-06 15:46 12M ensemblSource.sql 2014-04-06 15:46 1.4K ensemblSource.txt.gz 2014-04-06 15:46 235K ensemblToGeneName.sql 2014-04-06 15:46 1.4K ensemblToGeneName.txt.gz 2014-04-06 15:46 402K estOrientInfo.sql 2017-11-26 06:46 1.8K estOrientInfo.txt.gz 2017-11-26 06:47 20M extFile.sql 2011-10-09 10:33 1.4K extFile.txt.gz 2011-10-09 10:33 80 gap.sql 2011-01-19 10:54 1.5K gap.txt.gz 2011-01-19 10:54 325K gbLoaded.sql 2020-08-21 08:13 1.6K gbLoaded.txt.gz 2020-08-21 08:13 92K gc5BaseBw.sql 2011-01-19 11:08 1.2K gc5BaseBw.txt.gz 2011-01-19 11:08 63 genscan.sql 2013-12-09 21:01 1.7K genscan.txt.gz 2013-12-09 21:01 2.5M gold.sql 2011-01-19 11:16 1.6K gold.txt.gz 2011-01-19 11:16 692K grcIncidentDb.sql 2018-05-13 05:03 1.3K grcIncidentDb.txt.gz 2018-05-13 05:03 77 grp.sql 2014-03-02 03:40 1.3K grp.txt.gz 2014-03-02 03:40 209 hgFindSpec.sql 2020-12-06 07:52 1.7K hgFindSpec.txt.gz 2020-12-06 07:52 1.0K history.sql 2011-01-19 10:49 1.5K history.txt.gz 2011-01-19 10:49 249 intronEst.sql 2017-11-26 06:48 2.1K intronEst.txt.gz 2017-11-26 06:48 54M locusName.sql 2016-11-06 06:40 1.5K locusName.txt.gz 2016-11-06 06:40 4.3M mgcFullMrna.sql 2020-03-01 05:42 2.1K mgcFullMrna.txt.gz 2020-03-01 05:42 1.5M mgcGenes.sql 2020-03-01 05:42 1.9K mgcGenes.txt.gz 2020-03-01 05:42 1.2M microsat.sql 2015-08-23 13:32 1.5K microsat.txt.gz 2015-08-23 13:32 1.1M mrnaOrientInfo.sql 2020-08-21 08:12 1.8K mrnaOrientInfo.txt.gz 2020-08-21 08:12 807K multiz8way.sql 2011-10-09 10:34 1.5K multiz8way.txt.gz 2011-10-09 10:34 44M multiz8wayFrames.sql 2011-10-09 10:35 1.7K multiz8wayFrames.txt.gz 2011-10-09 10:36 26M multiz8waySummary.sql 2011-10-09 10:35 1.5K multiz8waySummary.txt.gz 2011-10-09 10:35 14M nestedRepeats.sql 2011-01-19 10:55 1.9K nestedRepeats.txt.gz 2011-01-19 10:55 8.1M netFr3.sql 2012-06-24 06:38 2.0K netFr3.txt.gz 2012-06-24 06:38 11M netGasAcu1.sql 2011-03-07 08:20 2.0K netGasAcu1.txt.gz 2011-03-07 08:20 16M netHg19.sql 2011-03-07 08:11 2.0K netHg19.txt.gz 2011-03-07 08:11 9.1M netMelGal1.sql 2011-11-06 09:58 2.0K netMelGal1.txt.gz 2011-11-06 09:58 4.9M netMm10.sql 2013-10-27 12:06 2.1K netMm10.txt.gz 2013-10-27 12:06 8.2M netOryLat2.sql 2011-03-07 06:59 2.0K netOryLat2.txt.gz 2011-03-07 06:59 14M netPanTro3.sql 2011-03-14 11:10 2.0K netPanTro3.txt.gz 2011-03-14 11:10 8.8M netTetNig2.sql 2011-03-07 08:11 2.0K netTetNig2.txt.gz 2011-03-07 08:11 9.5M netXenTro3.sql 2011-11-06 09:51 2.0K netXenTro3.txt.gz 2011-11-06 09:51 9.7M phastCons8way.sql 2011-10-09 10:34 1.7K phastCons8way.txt.gz 2011-10-09 10:34 16M phastCons8wayFish.sql 2011-10-09 10:33 1.7K phastCons8wayFish.txt.gz 2011-10-09 10:33 16M phastConsElements8way.sql 2011-10-09 10:34 1.5K phastConsElements8way.txt.gz 2011-10-09 10:34 11M phastConsElements8wayFish.sql 2011-10-09 10:33 1.5K phastConsElements8wayFish.txt.gz 2011-10-09 10:33 8.4M phyloP8way.sql 2011-10-09 10:33 1.7K phyloP8way.txt.gz 2011-10-09 10:33 16M phyloP8wayFish.sql 2011-10-09 10:35 1.7K phyloP8wayFish.txt.gz 2011-10-09 10:35 15M pubsBingBlat.sql 2014-01-26 10:26 2.4K pubsBingBlat.txt.gz 2014-01-26 10:26 1.1M pubsBingBlatPsl.sql 2014-01-26 10:26 2.2K pubsBingBlatPsl.txt.gz 2014-01-26 10:26 721K refFlat.sql 2020-08-21 08:12 1.7K refFlat.txt.gz 2020-08-21 08:12 1.5M refGene.sql 2020-08-21 08:12 1.9K refGene.txt.gz 2020-08-21 08:12 1.7M refSeqAli.sql 2020-08-21 08:12 2.1K refSeqAli.txt.gz 2020-08-21 08:12 1.7M rmsk.sql 2011-01-19 10:39 1.8K rmsk.txt.gz 2011-01-19 10:41 93M simpleRepeat.sql 2011-01-19 11:13 1.9K simpleRepeat.txt.gz 2011-01-19 11:13 26M tRNAs.sql 2012-04-22 21:28 1.7K tRNAs.txt.gz 2012-04-22 21:28 267K tableDescriptions.sql 2019-07-21 03:41 1.4K tableDescriptions.txt.gz 2019-07-21 03:41 8.6K tableList.sql 2021-05-02 03:11 1.6K tableList.txt.gz 2021-05-02 03:11 5.3K trackDb.sql 2020-12-02 17:16 2.0K trackDb.txt.gz 2020-12-02 17:16 54K ucscToINSDC.sql 2013-09-15 10:59 1.4K ucscToINSDC.txt.gz 2013-09-15 10:59 9.5K ucscToRefSeq.sql 2018-02-18 06:10 1.4K ucscToRefSeq.txt.gz 2018-02-18 06:10 9.7K xenoMrna.sql 2020-08-21 07:48 2.1K xenoMrna.txt.gz 2020-08-21 07:48 238M xenoRefFlat.sql 2020-08-21 08:12 1.7K xenoRefFlat.txt.gz 2020-08-21 08:12 22M xenoRefGene.sql 2020-08-21 08:12 1.9K xenoRefGene.txt.gz 2020-08-21 08:12 24M xenoRefSeqAli.sql 2020-08-21 08:12 2.1K xenoRefSeqAli.txt.gz 2020-08-21 08:12 22M