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 - chainHg19.sql 2011-04-16 12:11 1.6K chainHg19.txt.gz 2011-04-16 12:11 30M chainMonDom5.sql 2011-04-16 12:12 1.6K chainMonDom5.txt.gz 2011-04-16 12:12 32M netBosTau4.sql 2011-04-16 12:13 2.0K netBosTau4.txt.gz 2011-04-16 12:13 50M chainMonDom5Link.sql 2011-04-16 12:13 1.5K chainMonDom5Link.txt.gz 2011-04-16 12:14 105M ctgPos2.sql 2011-04-16 12:15 1.5K ctgPos2.txt.gz 2011-04-16 12:15 2.4K rmsk.sql 2011-04-16 12:18 1.8K rmsk.txt.gz 2011-04-16 12:19 51M netEquCab2.sql 2011-04-16 12:19 2.0K netEquCab2.txt.gz 2011-04-16 12:19 59M chainHg19Link.sql 2011-04-16 12:20 1.5K chainHg19Link.txt.gz 2011-04-16 12:21 272M chainBosTau4Link.sql 2011-04-16 12:24 1.5K chainBosTau4Link.txt.gz 2011-04-16 12:38 4.1G gc5Base.sql 2011-04-16 13:26 1.7K gc5Base.txt.gz 2011-04-16 13:27 11M gap.sql 2011-04-16 13:27 1.5K gap.txt.gz 2011-04-16 13:27 34M chainEquCab2Link.sql 2011-04-16 13:27 1.5K chainEquCab2Link.txt.gz 2011-04-16 13:29 631M netHg19.sql 2011-04-16 13:36 2.0K netHg19.txt.gz 2011-04-16 13:37 57M nestedRepeats.sql 2011-04-16 13:38 1.9K nestedRepeats.txt.gz 2011-04-16 13:38 3.4M chainEquCab2.sql 2011-04-16 13:38 1.6K chainEquCab2.txt.gz 2011-04-16 13:39 145M gold.sql 2011-04-16 13:40 1.6K gold.txt.gz 2011-04-16 13:40 36M history.sql 2011-04-16 13:40 1.5K history.txt.gz 2011-04-16 13:40 539 cpgIslandExt.sql 2011-04-16 13:40 1.6K cpgIslandExt.txt.gz 2011-04-16 13:40 545K simpleRepeat.sql 2011-04-16 13:41 1.9K simpleRepeat.txt.gz 2011-04-16 13:41 2.6M chromInfo.sql 2011-04-16 13:41 1.3K chromInfo.txt.gz 2011-04-16 13:41 8.5K netMonDom5.sql 2011-04-16 13:41 2.0K netMonDom5.txt.gz 2011-04-16 13:41 13M chainBosTau4.sql 2011-04-16 13:42 1.6K chainBosTau4.txt.gz 2011-04-16 13:49 2.2G tRNAs.sql 2012-04-16 03:44 1.7K tRNAs.txt.gz 2012-04-16 03:44 33K cytoBandIdeo.sql 2013-04-28 19:59 1.5K cytoBandIdeo.txt.gz 2013-04-28 19:59 7.5K 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 netMm10.sql 2013-10-27 19:46 2.1K netMm10.txt.gz 2013-10-27 19:47 37M grp.sql 2014-03-02 04:14 1.3K grp.txt.gz 2014-03-02 04:14 208 cpgIslandExtUnmasked.sql 2014-06-01 17:59 1.7K cpgIslandExtUnmasked.txt.gz 2014-06-01 17:59 579K augustusGene.sql 2015-07-26 17:21 1.9K augustusGene.txt.gz 2015-07-26 17:21 1.2M microsat.sql 2015-08-23 23:11 1.5K microsat.txt.gz 2015-08-23 23:11 32K xenoMrna.sql 2016-02-21 21:29 2.1K xenoMrna.txt.gz 2016-02-21 21:30 271M intronEst.sql 2016-05-15 11:01 2.1K intronEst.txt.gz 2016-05-15 11:01 6.0M estOrientInfo.sql 2016-05-15 11:01 1.8K estOrientInfo.txt.gz 2016-05-15 11:01 3.2M all_est.sql 2016-05-15 11:01 2.1K all_est.txt.gz 2016-05-15 11:01 12M tableDescriptions.sql 2019-07-21 03:43 1.4K tableDescriptions.txt.gz 2019-07-21 03:43 5.5K all_mrna.sql 2020-08-22 16:33 2.1K all_mrna.txt.gz 2020-08-22 16:33 170K refFlat.sql 2020-08-22 17:09 1.7K refGene.sql 2020-08-22 17:09 1.9K refGene.txt.gz 2020-08-22 17:09 75K refFlat.txt.gz 2020-08-22 17:09 66K xenoRefGene.sql 2020-08-22 17:09 1.9K xenoRefGene.txt.gz 2020-08-22 17:09 35M gbLoaded.sql 2020-08-22 17:09 1.6K mrnaOrientInfo.sql 2020-08-22 17:09 1.8K refSeqAli.sql 2020-08-22 17:09 2.1K xenoRefFlat.sql 2020-08-22 17:09 1.7K xenoRefSeqAli.sql 2020-08-22 17:09 2.1K xenoRefFlat.txt.gz 2020-08-22 17:09 31M mrnaOrientInfo.txt.gz 2020-08-22 17:09 58K refSeqAli.txt.gz 2020-08-22 17:09 82K xenoRefSeqAli.txt.gz 2020-08-22 17:09 33M gbLoaded.txt.gz 2020-08-22 17:09 43K trackDb.sql 2021-06-10 16:54 2.1K trackDb.txt.gz 2021-06-10 16:54 27K hgFindSpec.sql 2021-06-10 16:54 1.8K hgFindSpec.txt.gz 2021-06-10 16:54 534 tableList.sql 2021-06-13 03:15 1.6K tableList.txt.gz 2021-06-13 03:15 3.1K bigFiles.sql 2021-06-13 03:15 1.4K bigFiles.txt.gz 2021-06-13 03:15 33