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 - rmsk.sql 2011-01-19 10:39 1.8K rmsk.txt.gz 2011-01-19 10:41 93M history.sql 2011-01-19 10:49 1.5K history.txt.gz 2011-01-19 10:49 249 gap.sql 2011-01-19 10:54 1.5K gap.txt.gz 2011-01-19 10:54 325K chromInfo.sql 2011-01-19 10:55 1.3K chromInfo.txt.gz 2011-01-19 10:55 7.3K nestedRepeats.sql 2011-01-19 10:55 1.9K nestedRepeats.txt.gz 2011-01-19 10:55 8.1M gc5BaseBw.sql 2011-01-19 11:08 1.2K gc5BaseBw.txt.gz 2011-01-19 11:08 63 ctgPos2.sql 2011-01-19 11:12 1.5K ctgPos2.txt.gz 2011-01-19 11:12 13K simpleRepeat.sql 2011-01-19 11:13 1.9K simpleRepeat.txt.gz 2011-01-19 11:13 26M blastHg18KG.sql 2011-01-19 11:16 2.1K blastHg18KG.txt.gz 2011-01-19 11:16 3.1M gold.sql 2011-01-19 11:16 1.6K gold.txt.gz 2011-01-19 11:16 692K netOryLat2.sql 2011-03-07 06:59 2.0K netOryLat2.txt.gz 2011-03-07 06:59 14M chainTetNig2.sql 2011-03-07 06:59 1.6K chainTetNig2.txt.gz 2011-03-07 06:59 25M chainHg19Link.sql 2011-03-07 07:00 1.5K chainHg19Link.txt.gz 2011-03-07 07:05 1.0G chainTetNig2Link.sql 2011-03-07 07:19 1.5K chainTetNig2Link.txt.gz 2011-03-07 07:19 92M chainHg19.sql 2011-03-07 07:21 1.6K chainHg19.txt.gz 2011-03-07 07:23 317M chainGasAcu1.sql 2011-03-07 07:34 1.6K chainGasAcu1.txt.gz 2011-03-07 07:35 113M chainOryLat2Link.sql 2011-03-07 07:56 1.5K chainOryLat2Link.txt.gz 2011-03-07 07:57 313M chainGasAcu1Link.sql 2011-03-07 08:03 1.5K chainGasAcu1Link.txt.gz 2011-03-07 08:05 418M netHg19.sql 2011-03-07 08:11 2.0K netHg19.txt.gz 2011-03-07 08:11 9.1M netTetNig2.sql 2011-03-07 08:11 2.0K netTetNig2.txt.gz 2011-03-07 08:11 9.5M chainOryLat2.sql 2011-03-07 08:11 1.6K chainOryLat2.txt.gz 2011-03-07 08:12 76M netGasAcu1.sql 2011-03-07 08:20 2.0K netGasAcu1.txt.gz 2011-03-07 08:20 16M netPanTro3.sql 2011-03-14 11:10 2.0K netPanTro3.txt.gz 2011-03-14 11:10 8.8M chainPanTro3Link.sql 2011-03-14 11:10 1.5K chainPanTro3Link.txt.gz 2011-03-14 11:15 535M chainPanTro3.sql 2011-03-14 11:24 1.6K chainPanTro3.txt.gz 2011-03-14 11:25 161M cpgIslandExt.sql 2011-08-07 08:02 1.6K cpgIslandExt.txt.gz 2011-08-07 08:02 271K phastCons8wayFish.sql 2011-10-09 10:33 1.7K phastCons8wayFish.txt.gz 2011-10-09 10:33 16M phastConsElements8wayFish.sql 2011-10-09 10:33 1.5K phastConsElements8wayFish.txt.gz 2011-10-09 10:33 8.4M extFile.sql 2011-10-09 10:33 1.4K extFile.txt.gz 2011-10-09 10:33 80 phyloP8way.sql 2011-10-09 10:33 1.7K phyloP8way.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 phastCons8way.sql 2011-10-09 10:34 1.7K phastCons8way.txt.gz 2011-10-09 10:34 16M multiz8way.sql 2011-10-09 10:34 1.5K multiz8way.txt.gz 2011-10-09 10:34 44M phyloP8wayFish.sql 2011-10-09 10:35 1.7K phyloP8wayFish.txt.gz 2011-10-09 10:35 15M multiz8waySummary.sql 2011-10-09 10:35 1.5K multiz8waySummary.txt.gz 2011-10-09 10:35 14M multiz8wayFrames.sql 2011-10-09 10:35 1.7K multiz8wayFrames.txt.gz 2011-10-09 10:36 26M chainMelGal1Link.sql 2011-11-06 09:51 1.5K chainMelGal1Link.txt.gz 2011-11-06 09:51 19M UMassME1Peak.sql 2011-11-06 09:51 1.7K UMassME1Peak.txt.gz 2011-11-06 09:51 1.1M netXenTro3.sql 2011-11-06 09:51 2.0K netXenTro3.txt.gz 2011-11-06 09:51 9.7M UMassME1Hotspot.sql 2011-11-06 09:51 1.5K UMassME1Hotspot.txt.gz 2011-11-06 09:51 849K UMassME1.sql 2011-11-06 09:51 1.7K UMassME1.txt.gz 2011-11-06 09:51 2.4M UMassME3Hotspot.sql 2011-11-06 09:51 1.5K UMassME3Hotspot.txt.gz 2011-11-06 09:51 389K chainMelGal1.sql 2011-11-06 09:51 1.6K chainMelGal1.txt.gz 2011-11-06 09:51 5.3M chainXenTro3Link.sql 2011-11-06 09:51 1.5K chainXenTro3Link.txt.gz 2011-11-06 09:53 687M chainXenTro3.sql 2011-11-06 09:57 1.6K chainXenTro3.txt.gz 2011-11-06 09:57 222M UMassInput.sql 2011-11-06 09:58 1.7K UMassInput.txt.gz 2011-11-06 09:58 2.2M netMelGal1.sql 2011-11-06 09:58 2.0K netMelGal1.txt.gz 2011-11-06 09:58 4.9M UMassME3Peak.sql 2011-11-06 09:58 1.7K UMassME3Peak.txt.gz 2011-11-06 09:58 528K UMassME3.sql 2011-11-06 09:58 1.7K UMassME3.txt.gz 2011-11-06 09:58 1.1M tRNAs.sql 2012-04-22 21:28 1.7K tRNAs.txt.gz 2012-04-22 21:28 267K chainFr3.sql 2012-06-24 06:38 1.6K chainFr3.txt.gz 2012-06-24 06:38 29M netFr3.sql 2012-06-24 06:38 2.0K netFr3.txt.gz 2012-06-24 06:38 11M chainFr3Link.sql 2012-06-24 06:38 1.5K chainFr3Link.txt.gz 2012-06-24 06:39 115M cytoBandIdeo.sql 2013-04-28 12:53 1.5K cytoBandIdeo.txt.gz 2013-04-28 12:53 6.4K ucscToINSDC.sql 2013-09-15 10:59 1.4K ucscToINSDC.txt.gz 2013-09-15 10:59 9.5K 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 netMm10.sql 2013-10-27 12:06 2.1K netMm10.txt.gz 2013-10-27 12:06 8.2M genscan.sql 2013-12-09 21:01 1.7K genscan.txt.gz 2013-12-09 21:01 2.5M 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 grp.sql 2014-03-02 03:40 1.3K grp.txt.gz 2014-03-02 03:40 209 ensemblSource.sql 2014-04-06 15:46 1.4K ensemblSource.txt.gz 2014-04-06 15:46 235K 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 ensemblToGeneName.sql 2014-04-06 15:46 1.4K ensemblToGeneName.txt.gz 2014-04-06 15:46 402K ensGene.sql 2014-04-06 15:50 1.9K ensGene.txt.gz 2014-04-06 15:50 3.7M cpgIslandExtUnmasked.sql 2014-06-01 10:57 1.7K cpgIslandExtUnmasked.txt.gz 2014-06-01 10:57 1.0M augustusGene.sql 2015-07-26 11:52 1.9K augustusGene.txt.gz 2015-07-26 11:52 2.8M microsat.sql 2015-08-23 13:32 1.5K microsat.txt.gz 2015-08-23 13:32 1.1M 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 locusName.sql 2016-11-06 06:40 1.5K locusName.txt.gz 2016-11-06 06:40 4.3M estOrientInfo.sql 2017-11-26 06:46 1.8K estOrientInfo.txt.gz 2017-11-26 06:47 20M intronEst.sql 2017-11-26 06:48 2.1K intronEst.txt.gz 2017-11-26 06:48 54M all_est.sql 2017-11-26 06:48 2.1K all_est.txt.gz 2017-11-26 06:48 83M chromAlias.sql 2018-02-18 06:10 1.4K chromAlias.txt.gz 2018-02-18 06:10 5.7K ucscToRefSeq.sql 2018-02-18 06:10 1.4K ucscToRefSeq.txt.gz 2018-02-18 06:10 9.7K grcIncidentDb.sql 2018-05-13 05:03 1.3K grcIncidentDb.txt.gz 2018-05-13 05:03 77 mgcGenes.sql 2020-03-01 05:42 1.9K mgcGenes.txt.gz 2020-03-01 05:42 1.2M mgcFullMrna.sql 2020-03-01 05:42 2.1K mgcFullMrna.txt.gz 2020-03-01 05:42 1.5M all_mrna.sql 2020-08-21 07:48 2.1K all_mrna.txt.gz 2020-08-21 07:48 2.6M xenoMrna.sql 2020-08-21 07:48 2.1K xenoMrna.txt.gz 2020-08-21 07:48 238M refGene.sql 2020-08-21 08:12 1.9K refGene.txt.gz 2020-08-21 08:12 1.7M refFlat.sql 2020-08-21 08:12 1.7K refFlat.txt.gz 2020-08-21 08:12 1.5M xenoRefGene.sql 2020-08-21 08:12 2.0K xenoRefGene.txt.gz 2020-08-21 08:12 24M xenoRefFlat.sql 2020-08-21 08:12 1.7K xenoRefFlat.txt.gz 2020-08-21 08:12 22M mrnaOrientInfo.sql 2020-08-21 08:12 1.8K mrnaOrientInfo.txt.gz 2020-08-21 08:12 807K refSeqAli.sql 2020-08-21 08:12 2.1K refSeqAli.txt.gz 2020-08-21 08:12 1.7M xenoRefSeqAli.sql 2020-08-21 08:12 2.1K xenoRefSeqAli.txt.gz 2020-08-21 08:12 22M gbLoaded.sql 2020-08-21 08:13 1.6K gbLoaded.txt.gz 2020-08-21 08:13 92K trackDb.sql 2024-07-25 09:34 2.1K trackDb.txt.gz 2024-07-25 09:34 76K hgFindSpec.sql 2024-07-25 09:34 1.8K hgFindSpec.txt.gz 2024-07-25 09:34 1.1K tableDescriptions.sql 2024-12-07 02:03 1.4K tableDescriptions.txt.gz 2024-12-07 02:03 8.7K tableList.sql 2024-12-08 03:28 1.6K tableList.txt.gz 2024-12-08 03:28 5.4K bigFiles.sql 2024-12-08 03:28 1.4K bigFiles.txt.gz 2024-12-08 03:28 114