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 - bigFiles.txt.gz 2024-03-24 03:45 114 bigFiles.sql 2024-03-24 03:45 1.4K tableList.txt.gz 2024-03-24 03:45 5.6K tableList.sql 2024-03-24 03:45 1.6K tableDescriptions.txt.gz 2024-03-23 02:03 8.7K tableDescriptions.sql 2024-03-23 02:03 1.4K hgFindSpec.txt.gz 2023-09-19 16:08 1.1K hgFindSpec.sql 2023-09-19 16:08 1.8K trackDb.txt.gz 2023-09-19 16:08 64K trackDb.sql 2023-09-19 16:08 2.1K hgFindSpec_pushedout.txt.gz 2023-09-18 17:06 1.1K hgFindSpec_pushedout.sql 2023-09-18 17:06 1.8K trackDb_pushedout.txt.gz 2023-09-18 17:06 64K trackDb_pushedout.sql 2023-09-18 17:06 2.1K gbLoaded.txt.gz 2020-08-21 08:13 92K gbLoaded.sql 2020-08-21 08:13 1.6K xenoRefSeqAli.txt.gz 2020-08-21 08:12 22M xenoRefSeqAli.sql 2020-08-21 08:12 2.1K refSeqAli.txt.gz 2020-08-21 08:12 1.7M refSeqAli.sql 2020-08-21 08:12 2.1K mrnaOrientInfo.txt.gz 2020-08-21 08:12 807K mrnaOrientInfo.sql 2020-08-21 08:12 1.8K xenoRefFlat.txt.gz 2020-08-21 08:12 22M xenoRefFlat.sql 2020-08-21 08:12 1.7K xenoRefGene.txt.gz 2020-08-21 08:12 24M xenoRefGene.sql 2020-08-21 08:12 2.0K refFlat.txt.gz 2020-08-21 08:12 1.5M refFlat.sql 2020-08-21 08:12 1.7K refGene.txt.gz 2020-08-21 08:12 1.7M refGene.sql 2020-08-21 08:12 1.9K xenoMrna.txt.gz 2020-08-21 07:48 238M xenoMrna.sql 2020-08-21 07:48 2.1K all_mrna.txt.gz 2020-08-21 07:48 2.6M all_mrna.sql 2020-08-21 07:48 2.1K mgcFullMrna.txt.gz 2020-03-01 05:42 1.5M mgcFullMrna.sql 2020-03-01 05:42 2.1K mgcGenes.txt.gz 2020-03-01 05:42 1.2M mgcGenes.sql 2020-03-01 05:42 1.9K grcIncidentDb.txt.gz 2018-05-13 05:03 77 grcIncidentDb.sql 2018-05-13 05:03 1.3K ucscToRefSeq.txt.gz 2018-02-18 06:10 9.7K ucscToRefSeq.sql 2018-02-18 06:10 1.4K chromAlias.txt.gz 2018-02-18 06:10 5.7K chromAlias.sql 2018-02-18 06:10 1.4K all_est.txt.gz 2017-11-26 06:48 83M all_est.sql 2017-11-26 06:48 2.1K intronEst.txt.gz 2017-11-26 06:48 54M intronEst.sql 2017-11-26 06:48 2.1K estOrientInfo.txt.gz 2017-11-26 06:47 20M estOrientInfo.sql 2017-11-26 06:46 1.8K locusName.txt.gz 2016-11-06 06:40 4.3M locusName.sql 2016-11-06 06:40 1.5K crisprTargets.txt.gz 2016-11-06 06:40 63 crisprTargets.sql 2016-11-06 06:40 1.3K crisprRanges.txt.gz 2016-11-06 06:40 1.4M crisprRanges.sql 2016-11-06 06:40 1.4K microsat.txt.gz 2015-08-23 13:32 1.1M microsat.sql 2015-08-23 13:32 1.5K augustusGene.txt.gz 2015-07-26 11:52 2.8M augustusGene.sql 2015-07-26 11:52 1.9K cpgIslandExtUnmasked.txt.gz 2014-06-01 10:57 1.0M cpgIslandExtUnmasked.sql 2014-06-01 10:57 1.7K ensGene.txt.gz 2014-04-06 15:50 3.7M ensGene.sql 2014-04-06 15:50 1.9K ensemblToGeneName.txt.gz 2014-04-06 15:46 402K ensemblToGeneName.sql 2014-04-06 15:46 1.4K ensPep.txt.gz 2014-04-06 15:46 12M ensPep.sql 2014-04-06 15:46 1.3K ensGtp.txt.gz 2014-04-06 15:46 540K ensGtp.sql 2014-04-06 15:46 1.4K ensemblSource.txt.gz 2014-04-06 15:46 235K ensemblSource.sql 2014-04-06 15:46 1.4K grp.txt.gz 2014-03-02 03:40 209 grp.sql 2014-03-02 03:40 1.3K pubsBingBlatPsl.txt.gz 2014-01-26 10:26 721K pubsBingBlatPsl.sql 2014-01-26 10:26 2.2K pubsBingBlat.txt.gz 2014-01-26 10:26 1.1M pubsBingBlat.sql 2014-01-26 10:26 2.4K genscan.txt.gz 2013-12-09 21:01 2.5M genscan.sql 2013-12-09 21:01 1.7K netMm10.txt.gz 2013-10-27 12:06 8.2M netMm10.sql 2013-10-27 12:06 2.1K chainMm10Link.txt.gz 2013-10-27 12:05 234M chainMm10Link.sql 2013-10-27 12:05 1.5K chainMm10.txt.gz 2013-10-27 12:05 53M chainMm10.sql 2013-10-27 12:05 1.7K ucscToINSDC.txt.gz 2013-09-15 10:59 9.5K ucscToINSDC.sql 2013-09-15 10:59 1.4K cytoBandIdeo.txt.gz 2013-04-28 12:53 6.4K cytoBandIdeo.sql 2013-04-28 12:53 1.5K chainFr3Link.txt.gz 2012-06-24 06:39 115M chainFr3Link.sql 2012-06-24 06:38 1.5K netFr3.txt.gz 2012-06-24 06:38 11M netFr3.sql 2012-06-24 06:38 2.0K chainFr3.txt.gz 2012-06-24 06:38 29M chainFr3.sql 2012-06-24 06:38 1.6K tRNAs.txt.gz 2012-04-22 21:28 267K tRNAs.sql 2012-04-22 21:28 1.7K UMassME3.txt.gz 2011-11-06 09:58 1.1M UMassME3.sql 2011-11-06 09:58 1.7K UMassME3Peak.txt.gz 2011-11-06 09:58 528K UMassME3Peak.sql 2011-11-06 09:58 1.7K netMelGal1.txt.gz 2011-11-06 09:58 4.9M netMelGal1.sql 2011-11-06 09:58 2.0K UMassInput.txt.gz 2011-11-06 09:58 2.2M UMassInput.sql 2011-11-06 09:58 1.7K chainXenTro3.txt.gz 2011-11-06 09:57 222M chainXenTro3.sql 2011-11-06 09:57 1.6K chainXenTro3Link.txt.gz 2011-11-06 09:53 687M chainXenTro3Link.sql 2011-11-06 09:51 1.5K chainMelGal1.txt.gz 2011-11-06 09:51 5.3M chainMelGal1.sql 2011-11-06 09:51 1.6K UMassME3Hotspot.txt.gz 2011-11-06 09:51 389K UMassME3Hotspot.sql 2011-11-06 09:51 1.5K UMassME1.txt.gz 2011-11-06 09:51 2.4M UMassME1.sql 2011-11-06 09:51 1.7K UMassME1Hotspot.txt.gz 2011-11-06 09:51 849K UMassME1Hotspot.sql 2011-11-06 09:51 1.5K netXenTro3.txt.gz 2011-11-06 09:51 9.7M netXenTro3.sql 2011-11-06 09:51 2.0K UMassME1Peak.txt.gz 2011-11-06 09:51 1.1M UMassME1Peak.sql 2011-11-06 09:51 1.7K chainMelGal1Link.txt.gz 2011-11-06 09:51 19M chainMelGal1Link.sql 2011-11-06 09:51 1.5K multiz8wayFrames.txt.gz 2011-10-09 10:36 26M multiz8wayFrames.sql 2011-10-09 10:35 1.7K multiz8waySummary.txt.gz 2011-10-09 10:35 14M multiz8waySummary.sql 2011-10-09 10:35 1.5K phyloP8wayFish.txt.gz 2011-10-09 10:35 15M phyloP8wayFish.sql 2011-10-09 10:35 1.7K multiz8way.txt.gz 2011-10-09 10:34 44M multiz8way.sql 2011-10-09 10:34 1.5K phastCons8way.txt.gz 2011-10-09 10:34 16M phastCons8way.sql 2011-10-09 10:34 1.7K phastConsElements8way.txt.gz 2011-10-09 10:34 11M phastConsElements8way.sql 2011-10-09 10:34 1.5K phyloP8way.txt.gz 2011-10-09 10:33 16M phyloP8way.sql 2011-10-09 10:33 1.7K extFile.txt.gz 2011-10-09 10:33 80 extFile.sql 2011-10-09 10:33 1.4K phastConsElements8wayFish.txt.gz 2011-10-09 10:33 8.4M phastConsElements8wayFish.sql 2011-10-09 10:33 1.5K phastCons8wayFish.txt.gz 2011-10-09 10:33 16M phastCons8wayFish.sql 2011-10-09 10:33 1.7K cpgIslandExt.txt.gz 2011-08-07 08:02 271K cpgIslandExt.sql 2011-08-07 08:02 1.6K chainPanTro3.txt.gz 2011-03-14 11:25 161M chainPanTro3.sql 2011-03-14 11:24 1.6K chainPanTro3Link.txt.gz 2011-03-14 11:15 535M chainPanTro3Link.sql 2011-03-14 11:10 1.5K netPanTro3.txt.gz 2011-03-14 11:10 8.8M netPanTro3.sql 2011-03-14 11:10 2.0K netGasAcu1.txt.gz 2011-03-07 08:20 16M netGasAcu1.sql 2011-03-07 08:20 2.0K chainOryLat2.txt.gz 2011-03-07 08:12 76M chainOryLat2.sql 2011-03-07 08:11 1.6K netTetNig2.txt.gz 2011-03-07 08:11 9.5M netTetNig2.sql 2011-03-07 08:11 2.0K netHg19.txt.gz 2011-03-07 08:11 9.1M netHg19.sql 2011-03-07 08:11 2.0K chainGasAcu1Link.txt.gz 2011-03-07 08:05 418M chainGasAcu1Link.sql 2011-03-07 08:03 1.5K chainOryLat2Link.txt.gz 2011-03-07 07:57 313M chainOryLat2Link.sql 2011-03-07 07:56 1.5K chainGasAcu1.txt.gz 2011-03-07 07:35 113M chainGasAcu1.sql 2011-03-07 07:34 1.6K chainHg19.txt.gz 2011-03-07 07:23 317M chainHg19.sql 2011-03-07 07:21 1.6K chainTetNig2Link.txt.gz 2011-03-07 07:19 92M chainTetNig2Link.sql 2011-03-07 07:19 1.5K chainHg19Link.txt.gz 2011-03-07 07:05 1.0G chainHg19Link.sql 2011-03-07 07:00 1.5K chainTetNig2.txt.gz 2011-03-07 06:59 25M chainTetNig2.sql 2011-03-07 06:59 1.6K netOryLat2.txt.gz 2011-03-07 06:59 14M netOryLat2.sql 2011-03-07 06:59 2.0K gold.txt.gz 2011-01-19 11:16 692K gold.sql 2011-01-19 11:16 1.6K blastHg18KG.txt.gz 2011-01-19 11:16 3.1M blastHg18KG.sql 2011-01-19 11:16 2.1K simpleRepeat.txt.gz 2011-01-19 11:13 26M simpleRepeat.sql 2011-01-19 11:13 1.9K ctgPos2.txt.gz 2011-01-19 11:12 13K ctgPos2.sql 2011-01-19 11:12 1.5K gc5BaseBw.txt.gz 2011-01-19 11:08 63 gc5BaseBw.sql 2011-01-19 11:08 1.2K nestedRepeats.txt.gz 2011-01-19 10:55 8.1M nestedRepeats.sql 2011-01-19 10:55 1.9K chromInfo.txt.gz 2011-01-19 10:55 7.3K chromInfo.sql 2011-01-19 10:55 1.3K gap.txt.gz 2011-01-19 10:54 325K gap.sql 2011-01-19 10:54 1.5K history.txt.gz 2011-01-19 10:49 249 history.sql 2011-01-19 10:49 1.5K rmsk.txt.gz 2011-01-19 10:41 93M rmsk.sql 2011-01-19 10:39 1.8K