This directory contains a dump of the UCSC genome annotation database for
the Nov. 2009 (Bos_taurus_UMD_3.1/bosTau6) assembly of the cow genome (bosTau6, UMD_3.1 (NCBI project 10708, accession GCA_000003055.3)).
The annotations were generated by UCSC and collaborators worldwide.

This assembly was produced by the National Center for Biotechnology Information (NCBI).
For more information on the cow genome, see the project website:

http://www.ncbi.nlm.nih.gov/sites/entrez?Db=genomeprj&cmd=ShowDetailView&TermToSearch=10708

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=bosTau6
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/bosTau6/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/bosTau6/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/bosTau6/database/gc5BaseBw.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/bosTau6/database/*'
With wget, a single file: 
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/bosTau6/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 bosTau6 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql bosTau6 --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 2016-06-19 05:20 2.1K all_est.txt.gz 2016-06-19 05:20 62M all_mrna.sql 2020-08-20 21:43 2.1K all_mrna.txt.gz 2020-08-20 21:43 1.6M augustusGene.sql 2015-07-26 10:13 1.9K augustusGene.txt.gz 2015-07-26 10:13 2.3M bamAllNumtSSorted.sql 2013-08-18 03:44 1.3K bamAllNumtSSorted.txt.gz 2013-08-18 03:44 85 bigFiles.sql 2021-05-02 03:11 1.4K bigFiles.txt.gz 2021-05-02 03:11 109 chainCanFam2.sql 2011-11-02 16:10 1.6K chainCanFam2.txt.gz 2011-11-02 16:10 71M chainCanFam2Link.sql 2011-11-02 12:13 1.5K chainCanFam2Link.txt.gz 2011-11-02 12:18 650M chainHg19.sql 2011-11-02 11:01 1.6K chainHg19.txt.gz 2011-11-02 11:02 180M chainHg19Link.sql 2011-11-02 15:21 1.5K chainHg19Link.txt.gz 2011-11-02 15:26 835M chainMm9.sql 2011-11-02 11:05 1.6K chainMm9.txt.gz 2011-11-02 11:06 64M chainMm9Link.sql 2011-11-02 15:56 1.5K chainMm9Link.txt.gz 2011-11-02 15:59 491M chainMonDom5.sql 2011-11-02 15:39 1.6K chainMonDom5.txt.gz 2011-11-02 15:40 210M chainMonDom5Link.sql 2011-11-02 11:46 1.5K chainMonDom5Link.txt.gz 2011-11-02 11:50 656M chainOrnAna1.sql 2011-11-02 11:07 1.6K chainOrnAna1.txt.gz 2011-11-02 11:07 41M chainOrnAna1Link.sql 2011-11-02 15:10 1.5K chainOrnAna1Link.txt.gz 2011-11-02 15:11 234M chainRn4.sql 2011-11-02 15:38 1.6K chainRn4.txt.gz 2011-11-02 15:39 55M chainRn4Link.sql 2011-11-02 15:43 1.5K chainRn4Link.txt.gz 2011-11-02 15:46 455M chainSusScr2.sql 2011-11-02 11:08 1.6K chainSusScr2.txt.gz 2011-11-02 11:24 1.4G chainSusScr2Link.sql 2011-11-02 12:36 1.5K chainSusScr2Link.txt.gz 2011-11-02 13:33 6.9G chromAlias.sql 2018-08-05 05:27 1.4K chromAlias.txt.gz 2018-08-05 05:27 14K chromInfo.sql 2011-11-02 16:11 1.3K chromInfo.txt.gz 2011-11-02 16:11 16K cpgIslandExt.sql 2011-11-02 15:09 1.6K cpgIslandExt.txt.gz 2011-11-02 15:09 811K cpgIslandExtUnmasked.sql 2014-06-01 08:38 1.7K cpgIslandExtUnmasked.txt.gz 2014-06-01 08:38 924K ctgPos2.sql 2011-11-02 15:38 1.5K ctgPos2.txt.gz 2011-11-02 15:38 47K cytoBandIdeo.sql 2013-08-11 03:45 1.5K cytoBandIdeo.txt.gz 2013-08-11 03:45 16K ensGene.sql 2018-08-05 05:27 1.9K ensGene.txt.gz 2018-08-05 05:27 2.3M ensGtp.sql 2018-08-05 05:24 1.4K ensGtp.txt.gz 2018-08-05 05:24 311K ensPep.sql 2018-08-05 05:24 1.3K ensPep.txt.gz 2018-08-05 05:24 6.7M ensemblSource.sql 2018-08-05 05:24 1.4K ensemblSource.txt.gz 2018-08-05 05:24 86K ensemblToGeneName.sql 2018-08-05 05:27 1.4K ensemblToGeneName.txt.gz 2018-08-05 05:27 168K estOrientInfo.sql 2016-06-19 05:20 1.8K estOrientInfo.txt.gz 2016-06-19 05:20 19M gap.sql 2011-11-02 15:21 1.5K gap.txt.gz 2011-11-02 15:21 1.0M gbLoaded.sql 2020-08-20 21:48 1.6K gbLoaded.txt.gz 2020-08-20 21:48 107K gc5BaseBw.sql 2011-11-02 12:13 1.2K gc5BaseBw.txt.gz 2011-11-02 12:13 63 gold.sql 2011-11-02 15:52 1.6K gold.txt.gz 2011-11-02 15:52 1.3M grp.sql 2014-03-02 03:37 1.3K grp.txt.gz 2014-03-02 03:37 208 hgFindSpec.sql 2020-10-25 07:41 1.7K hgFindSpec.txt.gz 2020-10-25 07:41 829 history.sql 2011-11-02 15:21 1.5K history.txt.gz 2011-11-02 15:21 608 intronEst.sql 2016-06-19 05:20 2.1K intronEst.txt.gz 2016-06-19 05:21 37M microsat.sql 2015-08-23 10:22 1.5K microsat.txt.gz 2015-08-23 10:22 275K mrnaOrientInfo.sql 2020-08-20 21:48 1.8K mrnaOrientInfo.txt.gz 2020-08-20 21:48 595K nestedRepeats.sql 2011-11-02 12:36 1.9K nestedRepeats.txt.gz 2011-11-02 12:36 15M netCanFam2.sql 2011-11-02 12:11 2.0K netCanFam2.txt.gz 2011-11-02 12:12 71M netHg19.sql 2011-11-02 15:09 2.0K netHg19.txt.gz 2011-11-02 15:09 66M netMm9.sql 2011-11-02 15:17 2.0K netMm9.txt.gz 2011-11-02 15:18 54M netMonDom5.sql 2011-11-02 15:19 2.0K netMonDom5.txt.gz 2011-11-02 15:19 17M netOrnAna1.sql 2011-11-02 16:08 2.0K netOrnAna1.txt.gz 2011-11-02 16:08 17M netRn4.sql 2011-11-02 16:07 2.0K netRn4.txt.gz 2011-11-02 16:08 52M netSusScr2.sql 2011-11-02 16:08 2.0K netSusScr2.txt.gz 2011-11-02 16:09 65M numtS.sql 2013-08-18 03:44 1.7K numtS.txt.gz 2013-08-18 03:44 8.8K numtSAssembled.sql 2013-08-18 03:44 1.8K numtSAssembled.txt.gz 2013-08-18 03:44 2.7K numtSMitochondrion.sql 2013-08-18 03:44 1.6K numtSMitochondrion.txt.gz 2013-08-18 03:44 2.4K refFlat.sql 2020-08-20 21:48 1.7K refFlat.txt.gz 2020-08-20 21:48 1.4M refGene.sql 2020-08-20 21:48 1.9K refGene.txt.gz 2020-08-20 21:48 1.5M refSeqAli.sql 2020-08-20 21:48 2.1K refSeqAli.txt.gz 2020-08-20 21:48 1.5M rmsk.sql 2011-11-02 15:15 1.8K rmsk.txt.gz 2011-11-02 15:15 135M simpleRepeat.sql 2011-11-02 15:09 1.9K simpleRepeat.txt.gz 2011-11-02 15:09 12M tRNAs.sql 2012-04-15 15:40 1.7K tRNAs.txt.gz 2012-04-15 15:40 107K tableDescriptions.sql 2021-01-14 06:34 1.4K tableDescriptions.txt.gz 2021-01-14 06:34 6.1K tableList.sql 2021-05-02 03:11 1.6K tableList.txt.gz 2021-05-02 03:11 3.6K trackDb.sql 2020-10-25 07:41 2.0K trackDb.txt.gz 2020-10-25 07:41 35K ucscToEnsembl.sql 2011-11-02 12:36 1.3K ucscToEnsembl.txt.gz 2011-11-02 12:36 19K xenoMrna.sql 2020-08-20 21:43 2.1K xenoMrna.txt.gz 2020-08-20 21:43 346M xenoRefFlat.sql 2020-08-20 21:48 1.7K xenoRefFlat.txt.gz 2020-08-20 21:48 29M xenoRefGene.sql 2020-08-20 21:48 1.9K xenoRefGene.txt.gz 2020-08-20 21:48 32M xenoRefSeqAli.sql 2020-08-20 21:48 2.1K xenoRefSeqAli.txt.gz 2020-08-20 21:48 34M