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 - chainHg19.sql 2011-11-02 11:01 1.6K chainHg19.txt.gz 2011-11-02 11:02 180M chainMm9.sql 2011-11-02 11:05 1.6K chainMm9.txt.gz 2011-11-02 11:06 64M chainOrnAna1.sql 2011-11-02 11:07 1.6K chainOrnAna1.txt.gz 2011-11-02 11:07 41M chainSusScr2.sql 2011-11-02 11:08 1.6K chainSusScr2.txt.gz 2011-11-02 11:24 1.4G chainMonDom5Link.sql 2011-11-02 11:46 1.5K chainMonDom5Link.txt.gz 2011-11-02 11:50 656M netCanFam2.sql 2011-11-02 12:11 2.0K netCanFam2.txt.gz 2011-11-02 12:12 71M gc5BaseBw.sql 2011-11-02 12:13 1.2K gc5BaseBw.txt.gz 2011-11-02 12:13 63 chainCanFam2Link.sql 2011-11-02 12:13 1.5K chainCanFam2Link.txt.gz 2011-11-02 12:18 650M ucscToEnsembl.sql 2011-11-02 12:36 1.3K ucscToEnsembl.txt.gz 2011-11-02 12:36 19K nestedRepeats.sql 2011-11-02 12:36 1.9K nestedRepeats.txt.gz 2011-11-02 12:36 15M chainSusScr2Link.sql 2011-11-02 12:36 1.5K chainSusScr2Link.txt.gz 2011-11-02 13:33 6.9G cpgIslandExt.sql 2011-11-02 15:09 1.6K cpgIslandExt.txt.gz 2011-11-02 15:09 811K simpleRepeat.sql 2011-11-02 15:09 1.9K simpleRepeat.txt.gz 2011-11-02 15:09 12M netHg19.sql 2011-11-02 15:09 2.0K netHg19.txt.gz 2011-11-02 15:09 66M chainOrnAna1Link.sql 2011-11-02 15:10 1.5K chainOrnAna1Link.txt.gz 2011-11-02 15:11 234M rmsk.sql 2011-11-02 15:15 1.8K rmsk.txt.gz 2011-11-02 15:15 135M 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 history.sql 2011-11-02 15:21 1.5K history.txt.gz 2011-11-02 15:21 608 gap.sql 2011-11-02 15:21 1.5K gap.txt.gz 2011-11-02 15:21 1.0M chainHg19Link.sql 2011-11-02 15:21 1.5K chainHg19Link.txt.gz 2011-11-02 15:26 835M ctgPos2.sql 2011-11-02 15:38 1.5K ctgPos2.txt.gz 2011-11-02 15:38 47K chainRn4.sql 2011-11-02 15:38 1.6K chainRn4.txt.gz 2011-11-02 15:39 55M chainMonDom5.sql 2011-11-02 15:39 1.6K chainMonDom5.txt.gz 2011-11-02 15:40 210M chainRn4Link.sql 2011-11-02 15:43 1.5K chainRn4Link.txt.gz 2011-11-02 15:46 455M gold.sql 2011-11-02 15:52 1.6K gold.txt.gz 2011-11-02 15:52 1.3M chainMm9Link.sql 2011-11-02 15:56 1.5K chainMm9Link.txt.gz 2011-11-02 15:59 491M netRn4.sql 2011-11-02 16:07 2.0K netRn4.txt.gz 2011-11-02 16:08 52M netOrnAna1.sql 2011-11-02 16:08 2.0K netOrnAna1.txt.gz 2011-11-02 16:08 17M netSusScr2.sql 2011-11-02 16:08 2.0K netSusScr2.txt.gz 2011-11-02 16:09 65M chainCanFam2.sql 2011-11-02 16:10 1.6K chainCanFam2.txt.gz 2011-11-02 16:10 71M chromInfo.sql 2011-11-02 16:11 1.3K chromInfo.txt.gz 2011-11-02 16:11 16K tRNAs.sql 2012-04-15 15:40 1.7K tRNAs.txt.gz 2012-04-15 15:40 107K cytoBandIdeo.sql 2013-08-11 03:45 1.5K cytoBandIdeo.txt.gz 2013-08-11 03:45 16K bamAllNumtSSorted.sql 2013-08-18 03:44 1.3K bamAllNumtSSorted.txt.gz 2013-08-18 03:44 85 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 grp.sql 2014-03-02 03:37 1.3K grp.txt.gz 2014-03-02 03:37 208 cpgIslandExtUnmasked.sql 2014-06-01 08:38 1.7K cpgIslandExtUnmasked.txt.gz 2014-06-01 08:38 924K augustusGene.sql 2015-07-26 10:13 1.9K augustusGene.txt.gz 2015-07-26 10:13 2.3M microsat.sql 2015-08-23 10:22 1.5K microsat.txt.gz 2015-08-23 10:22 275K all_est.sql 2016-06-19 05:20 2.1K all_est.txt.gz 2016-06-19 05:20 62M estOrientInfo.sql 2016-06-19 05:20 1.8K estOrientInfo.txt.gz 2016-06-19 05:20 19M intronEst.sql 2016-06-19 05:20 2.1K intronEst.txt.gz 2016-06-19 05:21 37M 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 ensGene.sql 2018-08-05 05:27 1.9K ensGene.txt.gz 2018-08-05 05:27 2.3M chromAlias.sql 2018-08-05 05:27 1.4K chromAlias.txt.gz 2018-08-05 05:27 14K ensemblToGeneName.sql 2018-08-05 05:27 1.4K ensemblToGeneName.txt.gz 2018-08-05 05:27 168K all_mrna.sql 2020-08-20 21:43 2.1K all_mrna.txt.gz 2020-08-20 21:43 1.6M xenoMrna.sql 2020-08-20 21:43 2.1K xenoMrna.txt.gz 2020-08-20 21:43 346M gbLoaded.sql 2020-08-20 21:48 1.6K mrnaOrientInfo.sql 2020-08-20 21:48 1.8K refFlat.sql 2020-08-20 21:48 1.7K refGene.sql 2020-08-20 21:48 1.9K refSeqAli.sql 2020-08-20 21:48 2.1K xenoRefFlat.sql 2020-08-20 21:48 1.7K xenoRefGene.sql 2020-08-20 21:48 1.9K xenoRefSeqAli.sql 2020-08-20 21:48 2.1K refGene.txt.gz 2020-08-20 21:48 1.5M refFlat.txt.gz 2020-08-20 21:48 1.4M xenoRefGene.txt.gz 2020-08-20 21:48 32M xenoRefFlat.txt.gz 2020-08-20 21:48 29M mrnaOrientInfo.txt.gz 2020-08-20 21:48 595K refSeqAli.txt.gz 2020-08-20 21:48 1.5M xenoRefSeqAli.txt.gz 2020-08-20 21:48 34M gbLoaded.txt.gz 2020-08-20 21:48 107K tableDescriptions.sql 2021-01-14 06:34 1.4K tableDescriptions.txt.gz 2021-01-14 06:34 6.1K trackDb.sql 2021-12-27 12:20 2.1K trackDb.txt.gz 2021-12-27 12:20 37K hgFindSpec.sql 2021-12-27 12:20 1.8K hgFindSpec.txt.gz 2021-12-27 12:20 829 tableList.sql 2022-08-14 03:10 1.6K tableList.txt.gz 2022-08-14 03:10 3.6K bigFiles.sql 2022-08-14 03:10 1.4K bigFiles.txt.gz 2022-08-14 03:10 109