This directory contains a dump of the UCSC genome annotation database for the Mar. 2012 (RGSC 5.0/rn5) assembly of the rat genome (rn5, RGSC Rnor_5.0 (GCA_000001895.3)) from the Rat Genome Sequencing Consortium. The annotations were generated by UCSC and collaborators worldwide. For more information about this assembly, please note the NCBI resources: http://www.ncbi.nlm.nih.gov/genome/73 http://www.ncbi.nlm.nih.gov/genome/assembly/382928 http://www.ncbi.nlm.nih.gov/bioproject/16219 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=rn5 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/rn5/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/rn5/database/ . For a single file, e.g. gc5BaseBw.txt.gz rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/rn5/database/gc5BaseBw.txt.gz . Or with wget, all files: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/rn5/database/*' With wget, a single file: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/rn5/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 rn5 < chromInfo.sql ## load data from the txt.gz file $ zcat chromInfo.txt.gz | hgsql rn5 --local-infile=1 -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;' ------------------------------------------------------------------ These data are made available before scientific publication with the following understanding: 1. The data may be freely downloaded, used in analyses, and repackaged in databases. 2. Users are free to use the data in scientific papers analyzing particular genes and regions if the providers of this data (the Rat Genome Sequencing Consortium) are properly acknowledged. 3. The Centers producing the data reserve the right to publish the initial large-scale analyses of the dataset, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly. Large-scale refers to regions with size on the order of a chromosome (that is, 30 Mb or more). 4. This is in accordance with, and with the understandings in the Fort Lauderdale meeting discussing Community Resource Projects (see http://www.wellcome.ac.uk/en/1/awtpubrepdat.html) and the resulting NHGRI policy statement (http://www.genome.gov/page.cfm?pageID=10506537). 5. Any redistribution of the data should carry this notice.
Name Last modified Size Description
Parent Directory - all_est.sql 2016-05-15 11:25 2.1K all_est.txt.gz 2016-05-15 11:25 46M all_mrna.sql 2020-08-20 08:23 2.1K all_mrna.txt.gz 2020-08-20 08:23 4.1M augustusGene.sql 2015-07-26 17:21 1.9K augustusGene.txt.gz 2015-07-26 17:21 2.4M bigFiles.sql 2024-10-06 03:37 1.4K bigFiles.txt.gz 2024-10-06 03:37 86 chainMm10.sql 2012-06-17 21:29 1.6K chainMm10.txt.gz 2012-06-17 21:30 179M chainMm10Link.sql 2012-06-17 20:52 1.5K chainMm10Link.txt.gz 2012-06-17 20:59 1.0G chainPanTro4.sql 2014-01-26 18:29 1.7K chainPanTro4.txt.gz 2014-01-26 18:29 56M chainPanTro4Link.sql 2014-01-26 18:29 1.5K chainPanTro4Link.txt.gz 2014-01-26 18:30 485M chainRheMac3.sql 2012-12-02 21:09 1.7K chainRheMac3.txt.gz 2012-12-02 21:09 51M chainRheMac3Link.sql 2012-12-02 21:07 1.5K chainRheMac3Link.txt.gz 2012-12-02 21:07 444M chromAlias.sql 2016-09-15 18:03 1.4K chromAlias.txt.gz 2016-09-15 18:03 1.1K chromInfo.sql 2012-06-17 21:36 1.3K chromInfo.txt.gz 2012-06-17 21:36 16K cpgIslandExt.sql 2012-06-17 21:34 1.6K cpgIslandExt.txt.gz 2012-06-17 21:34 378K cpgIslandExtUnmasked.sql 2014-06-01 19:35 1.7K cpgIslandExtUnmasked.txt.gz 2014-06-01 19:35 447K crisprRanges.sql 2016-11-06 09:26 1.4K crisprRanges.txt.gz 2016-11-06 09:26 1.3M crisprTargets.sql 2016-11-06 09:26 1.3K crisprTargets.txt.gz 2016-11-06 09:26 59 cytoBand.sql 2013-07-28 06:10 1.5K cytoBand.txt.gz 2013-07-28 06:10 2.3K cytoBandIdeo.sql 2013-07-28 06:10 1.5K cytoBandIdeo.txt.gz 2013-07-28 06:10 17K ensGene.sql 2015-02-09 04:18 1.9K ensGene.txt.gz 2015-02-09 04:18 2.4M ensGtp.sql 2015-02-09 04:17 1.4K ensGtp.txt.gz 2015-02-09 04:17 308K ensPep.sql 2015-02-09 04:16 1.3K ensPep.txt.gz 2015-02-09 04:16 7.5M ensemblSource.sql 2015-02-09 04:17 1.3K ensemblSource.txt.gz 2015-02-09 04:17 89K ensemblToGeneName.sql 2015-02-09 04:17 1.4K ensemblToGeneName.txt.gz 2015-02-09 04:17 230K estOrientInfo.sql 2016-05-15 11:26 1.8K estOrientInfo.txt.gz 2016-05-15 11:26 13M extFile.sql 2014-06-22 17:01 1.4K extFile.txt.gz 2014-06-22 17:01 77 gap.sql 2012-06-17 21:32 1.5K gap.txt.gz 2012-06-17 21:32 2.9M gbLoaded.sql 2020-08-20 08:47 1.6K gbLoaded.txt.gz 2020-08-20 08:47 44K gc5BaseBw.sql 2012-06-17 21:28 1.2K gc5BaseBw.txt.gz 2012-06-17 21:28 59 genscan.sql 2012-06-17 21:29 1.6K genscan.txt.gz 2012-06-17 21:29 3.1M genscanSubopt.sql 2012-06-11 07:53 1.5K genscanSubopt.txt.gz 2012-06-11 07:54 6.6M gold.sql 2012-06-17 21:33 1.6K gold.txt.gz 2012-06-17 21:33 2.0M grp.sql 2014-03-02 04:14 1.3K grp.txt.gz 2014-03-02 04:14 208 hgFindSpec.sql 2024-07-25 09:34 1.8K hgFindSpec.txt.gz 2024-07-25 09:34 1.0K history.sql 2012-06-17 21:29 1.5K history.txt.gz 2012-06-17 21:29 391 intronEst.sql 2016-05-15 11:27 2.1K intronEst.txt.gz 2016-05-15 11:27 24M locusName.sql 2016-11-06 09:26 1.5K locusName.txt.gz 2016-11-06 09:26 3.4M mgcFullMrna.sql 2020-03-01 08:51 2.1K mgcFullMrna.txt.gz 2020-03-01 08:51 666K mgcGenes.sql 2020-03-01 08:52 1.9K mgcGenes.txt.gz 2020-03-01 08:52 614K microsat.sql 2015-08-24 01:15 1.5K microsat.txt.gz 2015-08-24 01:15 2.2M mrnaOrientInfo.sql 2020-08-20 08:47 1.8K mrnaOrientInfo.txt.gz 2020-08-20 08:47 1.7M multiz13way.sql 2014-06-22 17:01 1.5K multiz13way.txt.gz 2014-06-22 17:01 207M multiz13wayFrames.sql 2014-06-22 17:02 1.7K multiz13wayFrames.txt.gz 2014-06-22 17:02 23M multiz13waySummary.sql 2014-06-22 17:02 1.6K multiz13waySummary.txt.gz 2014-06-22 17:02 30M nestedRepeats.sql 2012-06-17 21:33 1.9K nestedRepeats.txt.gz 2012-06-17 21:33 11M netMm10.sql 2012-06-17 20:47 2.0K netMm10.txt.gz 2012-06-17 20:48 56M netPanTro4.sql 2014-01-26 18:32 2.1K netPanTro4.txt.gz 2014-01-26 18:32 51M netRheMac3.sql 2012-12-02 21:09 2.1K netRheMac3.txt.gz 2012-12-02 21:09 51M phastCons13way.sql 2014-06-22 17:02 1.8K phastCons13way.txt.gz 2014-06-22 17:02 65M phastConsElements13way.sql 2014-06-22 17:02 1.6K phastConsElements13way.txt.gz 2014-06-22 17:02 16M phyloP13way.sql 2014-06-22 17:03 1.8K phyloP13way.txt.gz 2014-06-22 17:03 72M refFlat.sql 2020-08-20 08:47 1.7K refFlat.txt.gz 2020-08-20 08:47 1.7M refGene.sql 2020-08-20 08:47 1.9K refGene.txt.gz 2020-08-20 08:47 1.9M refSeqAli.sql 2020-08-20 08:47 2.1K refSeqAli.txt.gz 2020-08-20 08:47 1.8M rmsk.sql 2012-06-17 21:29 1.8K rmsk.txt.gz 2012-06-17 21:30 123M simpleRepeat.sql 2012-06-17 21:37 1.9K simpleRepeat.txt.gz 2012-06-17 21:37 36M tableDescriptions.sql 2024-10-05 02:03 1.5K tableDescriptions.txt.gz 2024-10-05 02:03 6.7K tableList.sql 2024-10-06 03:37 1.6K tableList.txt.gz 2024-10-06 03:37 3.6K trackDb.sql 2024-07-25 09:34 2.1K trackDb.txt.gz 2024-07-25 09:34 60K ucscToINSDC.sql 2013-09-15 19:12 1.4K ucscToINSDC.txt.gz 2013-09-15 19:12 22K windowmaskerSdust.sql 2012-06-17 20:45 1.4K windowmaskerSdust.txt.gz 2012-06-17 20:43 127M xenoMrna.sql 2020-08-20 08:23 2.1K xenoMrna.txt.gz 2020-08-20 08:23 236M xenoRefFlat.sql 2020-08-20 08:47 1.7K xenoRefFlat.txt.gz 2020-08-20 08:47 22M xenoRefGene.sql 2020-08-20 08:47 1.9K xenoRefGene.txt.gz 2020-08-20 08:47 24M xenoRefSeqAli.sql 2020-08-20 08:47 2.1K xenoRefSeqAli.txt.gz 2020-08-20 08:47 24M