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 - crisprTargets.txt.gz 2016-11-06 06:40 63 gc5BaseBw.txt.gz 2011-01-19 11:08 63 grcIncidentDb.txt.gz 2018-05-13 05:03 77 extFile.txt.gz 2011-10-09 10:33 80 bigFiles.txt.gz 2024-12-08 03:28 114 grp.txt.gz 2014-03-02 03:40 209 history.txt.gz 2011-01-19 10:49 249 hgFindSpec.txt.gz 2024-07-25 09:34 1.1K gc5BaseBw.sql 2011-01-19 11:08 1.2K crisprTargets.sql 2016-11-06 06:40 1.3K grcIncidentDb.sql 2018-05-13 05:03 1.3K chromInfo.sql 2011-01-19 10:55 1.3K ensPep.sql 2014-04-06 15:46 1.3K grp.sql 2014-03-02 03:40 1.3K extFile.sql 2011-10-09 10:33 1.4K ensemblSource.sql 2014-04-06 15:46 1.4K bigFiles.sql 2024-12-08 03:28 1.4K ensemblToGeneName.sql 2014-04-06 15:46 1.4K chromAlias.sql 2018-02-18 06:10 1.4K tableDescriptions.sql 2024-12-07 02:03 1.4K ucscToINSDC.sql 2013-09-15 10:59 1.4K ucscToRefSeq.sql 2018-02-18 06:10 1.4K ensGtp.sql 2014-04-06 15:46 1.4K crisprRanges.sql 2016-11-06 06:40 1.4K multiz8way.sql 2011-10-09 10:34 1.5K chainFr3Link.sql 2012-06-24 06:38 1.5K chainHg19Link.sql 2011-03-07 07:00 1.5K ctgPos2.sql 2011-01-19 11:12 1.5K UMassME1Hotspot.sql 2011-11-06 09:51 1.5K UMassME3Hotspot.sql 2011-11-06 09:51 1.5K chainGasAcu1Link.sql 2011-03-07 08:03 1.5K chainMelGal1Link.sql 2011-11-06 09:51 1.5K chainOryLat2Link.sql 2011-03-07 07:56 1.5K chainPanTro3Link.sql 2011-03-14 11:10 1.5K chainTetNig2Link.sql 2011-03-07 07:19 1.5K chainXenTro3Link.sql 2011-11-06 09:51 1.5K microsat.sql 2015-08-23 13:32 1.5K locusName.sql 2016-11-06 06:40 1.5K phastConsElements8way.sql 2011-10-09 10:34 1.5K phastConsElements8wayFish.sql 2011-10-09 10:33 1.5K history.sql 2011-01-19 10:49 1.5K multiz8waySummary.sql 2011-10-09 10:35 1.5K cytoBandIdeo.sql 2013-04-28 12:53 1.5K gap.sql 2011-01-19 10:54 1.5K chainMm10Link.sql 2013-10-27 12:05 1.5K tableList.sql 2024-12-08 03:28 1.6K gold.sql 2011-01-19 11:16 1.6K gbLoaded.sql 2020-08-21 08:13 1.6K cpgIslandExt.sql 2011-08-07 08:02 1.6K chainFr3.sql 2012-06-24 06:38 1.6K chainHg19.sql 2011-03-07 07:21 1.6K chainGasAcu1.sql 2011-03-07 07:34 1.6K chainMelGal1.sql 2011-11-06 09:51 1.6K chainOryLat2.sql 2011-03-07 08:11 1.6K chainPanTro3.sql 2011-03-14 11:24 1.6K chainTetNig2.sql 2011-03-07 06:59 1.6K chainXenTro3.sql 2011-11-06 09:57 1.6K multiz8wayFrames.sql 2011-10-09 10:35 1.7K genscan.sql 2013-12-09 21:01 1.7K tRNAs.sql 2012-04-22 21:28 1.7K UMassME1.sql 2011-11-06 09:51 1.7K UMassME3.sql 2011-11-06 09:58 1.7K UMassInput.sql 2011-11-06 09:58 1.7K phyloP8way.sql 2011-10-09 10:33 1.7K UMassME1Peak.sql 2011-11-06 09:51 1.7K UMassME3Peak.sql 2011-11-06 09:58 1.7K phastCons8way.sql 2011-10-09 10:34 1.7K chainMm10.sql 2013-10-27 12:05 1.7K phyloP8wayFish.sql 2011-10-09 10:35 1.7K cpgIslandExtUnmasked.sql 2014-06-01 10:57 1.7K phastCons8wayFish.sql 2011-10-09 10:33 1.7K refFlat.sql 2020-08-21 08:12 1.7K xenoRefFlat.sql 2020-08-21 08:12 1.7K hgFindSpec.sql 2024-07-25 09:34 1.8K estOrientInfo.sql 2017-11-26 06:46 1.8K rmsk.sql 2011-01-19 10:39 1.8K mrnaOrientInfo.sql 2020-08-21 08:12 1.8K simpleRepeat.sql 2011-01-19 11:13 1.9K nestedRepeats.sql 2011-01-19 10:55 1.9K ensGene.sql 2014-04-06 15:50 1.9K mgcGenes.sql 2020-03-01 05:42 1.9K augustusGene.sql 2015-07-26 11:52 1.9K refGene.sql 2020-08-21 08:12 1.9K xenoRefGene.sql 2020-08-21 08:12 2.0K netFr3.sql 2012-06-24 06:38 2.0K netHg19.sql 2011-03-07 08:11 2.0K netGasAcu1.sql 2011-03-07 08:20 2.0K netMelGal1.sql 2011-11-06 09:58 2.0K netOryLat2.sql 2011-03-07 06:59 2.0K netPanTro3.sql 2011-03-14 11:10 2.0K netTetNig2.sql 2011-03-07 08:11 2.0K netXenTro3.sql 2011-11-06 09:51 2.0K blastHg18KG.sql 2011-01-19 11:16 2.1K trackDb.sql 2024-07-25 09:34 2.1K netMm10.sql 2013-10-27 12:06 2.1K all_est.sql 2017-11-26 06:48 2.1K intronEst.sql 2017-11-26 06:48 2.1K mgcFullMrna.sql 2020-03-01 05:42 2.1K all_mrna.sql 2020-08-21 07:48 2.1K xenoMrna.sql 2020-08-21 07:48 2.1K refSeqAli.sql 2020-08-21 08:12 2.1K xenoRefSeqAli.sql 2020-08-21 08:12 2.1K pubsBingBlatPsl.sql 2014-01-26 10:26 2.2K pubsBingBlat.sql 2014-01-26 10:26 2.4K tableList.txt.gz 2024-12-08 03:28 5.4K chromAlias.txt.gz 2018-02-18 06:10 5.7K cytoBandIdeo.txt.gz 2013-04-28 12:53 6.4K chromInfo.txt.gz 2011-01-19 10:55 7.3K tableDescriptions.txt.gz 2024-12-07 02:03 8.7K ucscToINSDC.txt.gz 2013-09-15 10:59 9.5K ucscToRefSeq.txt.gz 2018-02-18 06:10 9.7K ctgPos2.txt.gz 2011-01-19 11:12 13K trackDb.txt.gz 2024-07-25 09:34 76K gbLoaded.txt.gz 2020-08-21 08:13 92K ensemblSource.txt.gz 2014-04-06 15:46 235K tRNAs.txt.gz 2012-04-22 21:28 267K cpgIslandExt.txt.gz 2011-08-07 08:02 271K gap.txt.gz 2011-01-19 10:54 325K UMassME3Hotspot.txt.gz 2011-11-06 09:51 389K ensemblToGeneName.txt.gz 2014-04-06 15:46 402K UMassME3Peak.txt.gz 2011-11-06 09:58 528K ensGtp.txt.gz 2014-04-06 15:46 540K gold.txt.gz 2011-01-19 11:16 692K pubsBingBlatPsl.txt.gz 2014-01-26 10:26 721K mrnaOrientInfo.txt.gz 2020-08-21 08:12 807K UMassME1Hotspot.txt.gz 2011-11-06 09:51 849K cpgIslandExtUnmasked.txt.gz 2014-06-01 10:57 1.0M UMassME3.txt.gz 2011-11-06 09:58 1.1M UMassME1Peak.txt.gz 2011-11-06 09:51 1.1M microsat.txt.gz 2015-08-23 13:32 1.1M pubsBingBlat.txt.gz 2014-01-26 10:26 1.1M mgcGenes.txt.gz 2020-03-01 05:42 1.2M crisprRanges.txt.gz 2016-11-06 06:40 1.4M refFlat.txt.gz 2020-08-21 08:12 1.5M mgcFullMrna.txt.gz 2020-03-01 05:42 1.5M refSeqAli.txt.gz 2020-08-21 08:12 1.7M refGene.txt.gz 2020-08-21 08:12 1.7M UMassInput.txt.gz 2011-11-06 09:58 2.2M UMassME1.txt.gz 2011-11-06 09:51 2.4M genscan.txt.gz 2013-12-09 21:01 2.5M all_mrna.txt.gz 2020-08-21 07:48 2.6M augustusGene.txt.gz 2015-07-26 11:52 2.8M blastHg18KG.txt.gz 2011-01-19 11:16 3.1M ensGene.txt.gz 2014-04-06 15:50 3.7M locusName.txt.gz 2016-11-06 06:40 4.3M netMelGal1.txt.gz 2011-11-06 09:58 4.9M chainMelGal1.txt.gz 2011-11-06 09:51 5.3M nestedRepeats.txt.gz 2011-01-19 10:55 8.1M netMm10.txt.gz 2013-10-27 12:06 8.2M phastConsElements8wayFish.txt.gz 2011-10-09 10:33 8.4M netPanTro3.txt.gz 2011-03-14 11:10 8.8M netHg19.txt.gz 2011-03-07 08:11 9.1M netTetNig2.txt.gz 2011-03-07 08:11 9.5M netXenTro3.txt.gz 2011-11-06 09:51 9.7M netFr3.txt.gz 2012-06-24 06:38 11M phastConsElements8way.txt.gz 2011-10-09 10:34 11M ensPep.txt.gz 2014-04-06 15:46 12M multiz8waySummary.txt.gz 2011-10-09 10:35 14M netOryLat2.txt.gz 2011-03-07 06:59 14M phyloP8wayFish.txt.gz 2011-10-09 10:35 15M netGasAcu1.txt.gz 2011-03-07 08:20 16M phastCons8wayFish.txt.gz 2011-10-09 10:33 16M phyloP8way.txt.gz 2011-10-09 10:33 16M phastCons8way.txt.gz 2011-10-09 10:34 16M chainMelGal1Link.txt.gz 2011-11-06 09:51 19M estOrientInfo.txt.gz 2017-11-26 06:47 20M xenoRefFlat.txt.gz 2020-08-21 08:12 22M xenoRefSeqAli.txt.gz 2020-08-21 08:12 22M xenoRefGene.txt.gz 2020-08-21 08:12 24M chainTetNig2.txt.gz 2011-03-07 06:59 25M simpleRepeat.txt.gz 2011-01-19 11:13 26M multiz8wayFrames.txt.gz 2011-10-09 10:36 26M chainFr3.txt.gz 2012-06-24 06:38 29M multiz8way.txt.gz 2011-10-09 10:34 44M chainMm10.txt.gz 2013-10-27 12:05 53M intronEst.txt.gz 2017-11-26 06:48 54M chainOryLat2.txt.gz 2011-03-07 08:12 76M all_est.txt.gz 2017-11-26 06:48 83M chainTetNig2Link.txt.gz 2011-03-07 07:19 92M rmsk.txt.gz 2011-01-19 10:41 93M chainGasAcu1.txt.gz 2011-03-07 07:35 113M chainFr3Link.txt.gz 2012-06-24 06:39 115M chainPanTro3.txt.gz 2011-03-14 11:25 161M chainXenTro3.txt.gz 2011-11-06 09:57 222M chainMm10Link.txt.gz 2013-10-27 12:05 234M xenoMrna.txt.gz 2020-08-21 07:48 238M chainOryLat2Link.txt.gz 2011-03-07 07:57 313M chainHg19.txt.gz 2011-03-07 07:23 317M chainGasAcu1Link.txt.gz 2011-03-07 08:05 418M chainPanTro3Link.txt.gz 2011-03-14 11:15 535M chainXenTro3Link.txt.gz 2011-11-06 09:53 687M chainHg19Link.txt.gz 2011-03-07 07:05 1.0G