This directory contains a dump of the UCSC genome annotation database for the Feb. 2010 (ISGC Ovis_aries_1.0/oviAri1) assembly of the sheep genome (oviAri1, ISGC (NCBI project 10709, accession GCA_000005525.1)). The annotations were generated by UCSC and collaborators worldwide. This assembly was produced by the International Sheep Genomics Consortium (ISGC). For more information on the sheep genome, see the project website: http://www.sheephapmap.org/ http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=33937 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=oviAri1 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/oviAri1/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/oviAri1/database/ . For a single file, e.g. gc5BaseBw.txt.gz rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/oviAri1/database/gc5BaseBw.txt.gz . Or with wget, all files: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/oviAri1/database/*' With wget, a single file: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/oviAri1/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 oviAri1 < chromInfo.sql ## load data from the txt.gz file $ zcat chromInfo.txt.gz | hgsql oviAri1 --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 - all_est.sql 2016-05-15 11:01 2.1K all_est.txt.gz 2016-05-15 11:01 12M all_mrna.sql 2020-08-22 16:33 2.1K all_mrna.txt.gz 2020-08-22 16:33 170K augustusGene.sql 2015-07-26 17:21 1.9K augustusGene.txt.gz 2015-07-26 17:21 1.2M bigFiles.sql 2024-10-06 03:36 1.4K bigFiles.txt.gz 2024-10-06 03:36 33 chainBosTau4.sql 2011-04-16 13:42 1.6K chainBosTau4.txt.gz 2011-04-16 13:49 2.2G chainBosTau4Link.sql 2011-04-16 12:24 1.5K chainBosTau4Link.txt.gz 2011-04-16 12:38 4.1G chainEquCab2.sql 2011-04-16 13:38 1.6K chainEquCab2.txt.gz 2011-04-16 13:39 145M chainEquCab2Link.sql 2011-04-16 13:27 1.5K chainEquCab2Link.txt.gz 2011-04-16 13:29 631M chainHg19.sql 2011-04-16 12:11 1.6K chainHg19.txt.gz 2011-04-16 12:11 30M chainHg19Link.sql 2011-04-16 12:20 1.5K chainHg19Link.txt.gz 2011-04-16 12:21 272M chainMm10.sql 2013-10-27 19:46 1.7K chainMm10.txt.gz 2013-10-27 19:46 14M chainMm10Link.sql 2013-10-27 19:46 1.5K chainMm10Link.txt.gz 2013-10-27 19:46 152M chainMonDom5.sql 2011-04-16 12:12 1.6K chainMonDom5.txt.gz 2011-04-16 12:12 32M chainMonDom5Link.sql 2011-04-16 12:13 1.5K chainMonDom5Link.txt.gz 2011-04-16 12:14 105M chromInfo.sql 2011-04-16 13:41 1.3K chromInfo.txt.gz 2011-04-16 13:41 8.5K cpgIslandExt.sql 2011-04-16 13:40 1.6K cpgIslandExt.txt.gz 2011-04-16 13:40 545K cpgIslandExtUnmasked.sql 2014-06-01 17:59 1.7K cpgIslandExtUnmasked.txt.gz 2014-06-01 17:59 579K ctgPos2.sql 2011-04-16 12:15 1.5K ctgPos2.txt.gz 2011-04-16 12:15 2.4K cytoBandIdeo.sql 2013-04-28 19:59 1.5K cytoBandIdeo.txt.gz 2013-04-28 19:59 7.5K estOrientInfo.sql 2016-05-15 11:01 1.8K estOrientInfo.txt.gz 2016-05-15 11:01 3.2M gap.sql 2011-04-16 13:27 1.5K gap.txt.gz 2011-04-16 13:27 34M gbLoaded.sql 2020-08-22 17:09 1.6K gbLoaded.txt.gz 2020-08-22 17:09 43K gc5Base.sql 2011-04-16 13:26 1.7K gc5Base.txt.gz 2011-04-16 13:27 11M gold.sql 2011-04-16 13:40 1.6K gold.txt.gz 2011-04-16 13:40 36M grp.sql 2014-03-02 04:14 1.3K grp.txt.gz 2014-03-02 04:14 208 hgFindSpec.sql 2023-03-28 13:52 1.8K hgFindSpec.txt.gz 2023-03-28 13:52 582 history.sql 2011-04-16 13:40 1.5K history.txt.gz 2011-04-16 13:40 539 intronEst.sql 2016-05-15 11:01 2.1K intronEst.txt.gz 2016-05-15 11:01 6.0M microsat.sql 2015-08-23 23:11 1.5K microsat.txt.gz 2015-08-23 23:11 32K mrnaOrientInfo.sql 2020-08-22 17:09 1.8K mrnaOrientInfo.txt.gz 2020-08-22 17:09 58K nestedRepeats.sql 2011-04-16 13:38 1.9K nestedRepeats.txt.gz 2011-04-16 13:38 3.4M netBosTau4.sql 2011-04-16 12:13 2.0K netBosTau4.txt.gz 2011-04-16 12:13 50M netEquCab2.sql 2011-04-16 12:19 2.0K netEquCab2.txt.gz 2011-04-16 12:19 59M netHg19.sql 2011-04-16 13:36 2.0K netHg19.txt.gz 2011-04-16 13:37 57M netMm10.sql 2013-10-27 19:46 2.1K netMm10.txt.gz 2013-10-27 19:47 37M netMonDom5.sql 2011-04-16 13:41 2.0K netMonDom5.txt.gz 2011-04-16 13:41 13M refFlat.sql 2020-08-22 17:09 1.7K refFlat.txt.gz 2020-08-22 17:09 66K refGene.sql 2020-08-22 17:09 1.9K refGene.txt.gz 2020-08-22 17:09 75K refSeqAli.sql 2020-08-22 17:09 2.1K refSeqAli.txt.gz 2020-08-22 17:09 82K rmsk.sql 2011-04-16 12:18 1.8K rmsk.txt.gz 2011-04-16 12:19 51M simpleRepeat.sql 2011-04-16 13:41 1.9K simpleRepeat.txt.gz 2011-04-16 13:41 2.6M tRNAs.sql 2012-04-16 03:44 1.7K tRNAs.txt.gz 2012-04-16 03:44 33K tableDescriptions.sql 2024-10-05 02:03 1.5K tableDescriptions.txt.gz 2024-10-05 02:03 5.7K tableList.sql 2024-10-06 03:36 1.6K tableList.txt.gz 2024-10-06 03:36 3.1K trackDb.sql 2023-03-28 13:52 2.1K trackDb.txt.gz 2023-03-28 13:52 28K xenoMrna.sql 2016-02-21 21:29 2.1K xenoMrna.txt.gz 2016-02-21 21:30 271M xenoRefFlat.sql 2020-08-22 17:09 1.7K xenoRefFlat.txt.gz 2020-08-22 17:09 31M xenoRefGene.sql 2020-08-22 17:09 2.0K xenoRefGene.txt.gz 2020-08-22 17:09 35M xenoRefSeqAli.sql 2020-08-22 17:09 2.1K xenoRefSeqAli.txt.gz 2020-08-22 17:09 33M