This directory contains a dump of the UCSC genome annotation database for
the Oct. 2011 (Btau_4.6.1/bosTau7) assembly of the cow genome (bosTau7, Btau_4.6.1 (NCBI project 12555, accession GCA_000003205.4)).
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/bioproject/12555

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=bosTau7
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/bosTau7/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/bosTau7/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/bosTau7/database/gc5BaseBw.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/bosTau7/database/*'
With wget, a single file: 
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/bosTau7/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 bosTau7 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql bosTau7 --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 - chainTurTru2Link.txt.gz 2012-12-02 10:15 4.3G chainVicPac1Link.txt.gz 2012-11-18 10:18 3.1G chainSusScr2Link.txt.gz 2012-06-10 22:42 3.1G chainTurTru2.txt.gz 2012-12-02 10:03 1.7G chainCerSim1Link.txt.gz 2013-01-29 14:47 1.6G chainVicPac1.txt.gz 2012-11-18 10:31 1.0G chainHg19Link.txt.gz 2012-06-10 13:52 907M chainMonDom5Link.txt.gz 2012-06-11 02:18 763M chainSusScr2.txt.gz 2012-06-10 15:46 749M chainCanFam2Link.txt.gz 2012-06-11 03:37 681M chainMm10Link.txt.gz 2012-06-10 17:39 530M chainRn4Link.txt.gz 2012-06-10 20:47 508M chainCerSim1.txt.gz 2013-01-29 14:53 365M snp138.txt.gz 2014-03-02 03:39 338M xenoMrna.txt.gz 2020-08-20 21:06 313M chainOrnAna1Link.txt.gz 2012-06-11 01:31 257M chainMonDom5.txt.gz 2012-06-10 20:14 247M chainHg19.txt.gz 2012-06-10 19:10 202M rmsk.txt.gz 2012-06-10 18:50 144M snp138Seq.txt.gz 2014-03-02 03:37 136M windowmaskerSdust.txt.gz 2012-06-10 16:58 121M chainCanFam2.txt.gz 2012-06-11 01:58 75M netCanFam2.txt.gz 2012-06-10 16:45 74M chainMm10.txt.gz 2012-06-10 17:19 73M netHg19.txt.gz 2012-06-11 01:51 68M netCerSim1.txt.gz 2013-01-29 14:44 67M netTurTru2.txt.gz 2012-12-02 10:08 67M netSusScr2.txt.gz 2012-06-11 03:13 66M netVicPac1.txt.gz 2012-11-18 10:34 66M chainRn4.txt.gz 2012-06-10 17:10 66M all_est.txt.gz 2016-06-19 05:26 64M netMm10.txt.gz 2012-06-10 21:33 56M netRn4.txt.gz 2012-06-10 21:26 54M chainOrnAna1.txt.gz 2012-06-10 16:37 46M snp138Mult.txt.gz 2014-03-02 03:40 40M intronEst.txt.gz 2016-06-19 05:25 38M xenoRefGene.txt.gz 2020-08-20 21:21 33M xenoRefSeqAli.txt.gz 2020-08-20 21:26 32M xenoRefFlat.txt.gz 2020-08-20 21:21 29M estOrientInfo.txt.gz 2016-06-19 05:25 20M netOrnAna1.txt.gz 2012-06-11 03:21 18M netMonDom5.txt.gz 2012-06-10 18:25 18M nestedRepeats.txt.gz 2012-06-11 02:02 16M simpleRepeat.txt.gz 2012-06-10 19:21 13M genscanSubopt.txt.gz 2012-06-10 20:38 6.1M pubsBingBlat.txt.gz 2014-01-26 08:18 3.2M genscan.txt.gz 2012-06-11 04:40 3.1M gold.txt.gz 2012-06-10 20:08 2.4M augustusGene.txt.gz 2015-07-26 10:20 2.4M pubsBingBlatPsl.txt.gz 2014-01-26 08:18 2.1M snp138CodingDbSnp.txt.gz 2014-03-02 03:40 2.1M all_mrna.txt.gz 2020-08-20 21:06 1.6M refSeqAli.txt.gz 2020-08-20 21:26 1.5M refGene.txt.gz 2020-08-20 21:21 1.5M refFlat.txt.gz 2020-08-20 21:21 1.4M gap.txt.gz 2012-06-10 18:46 1.0M cpgIslandExtUnmasked.txt.gz 2014-06-01 08:44 957K cpgIslandExt.txt.gz 2012-06-10 18:59 824K mrnaOrientInfo.txt.gz 2020-08-20 21:22 598K snp138Common.txt.gz 2014-03-02 03:40 395K microsat.txt.gz 2015-08-23 10:30 313K ucscToINSDC.txt.gz 2013-09-15 08:53 97K animalQtl.txt.gz 2014-06-29 15:28 79K chromInfo.txt.gz 2012-06-10 20:27 75K cytoBandIdeo.txt.gz 2013-04-28 10:33 71K chromAlias.txt.gz 2016-09-15 17:55 70K trackDb.txt.gz 2021-12-17 16:13 60K gbLoaded.txt.gz 2020-08-20 21:41 45K ctgPos2.txt.gz 2012-06-10 17:06 28K tableDescriptions.txt.gz 2020-10-10 02:03 8.0K tableList.txt.gz 2022-10-02 03:11 5.1K snp138Common.sql 2014-03-02 03:40 3.0K snp138Mult.sql 2014-03-02 03:40 3.0K snp138.sql 2014-03-02 03:38 3.0K pubsBingBlat.sql 2014-01-26 08:18 2.4K pubsBingBlatPsl.sql 2014-01-26 08:18 2.2K xenoRefSeqAli.sql 2020-08-20 21:26 2.1K refSeqAli.sql 2020-08-20 21:26 2.1K intronEst.sql 2016-06-19 05:25 2.1K xenoMrna.sql 2020-08-20 21:06 2.1K all_mrna.sql 2020-08-20 21:06 2.1K all_est.sql 2016-06-19 05:26 2.1K netVicPac1.sql 2012-11-18 10:34 2.1K netTurTru2.sql 2012-12-02 10:08 2.1K netCerSim1.sql 2013-01-29 14:43 2.1K trackDb.sql 2021-12-17 16:13 2.1K netSusScr2.sql 2012-06-11 03:11 2.0K netOrnAna1.sql 2012-06-11 03:20 2.0K netMonDom5.sql 2012-06-10 18:24 2.0K netCanFam2.sql 2012-06-10 16:41 2.0K netMm10.sql 2012-06-10 21:30 2.0K netHg19.sql 2012-06-11 01:49 2.0K netRn4.sql 2012-06-10 21:24 2.0K augustusGene.sql 2015-07-26 10:20 1.9K xenoRefGene.sql 2020-08-20 21:21 1.9K refGene.sql 2020-08-20 21:21 1.9K nestedRepeats.sql 2012-06-11 02:02 1.9K simpleRepeat.sql 2012-06-10 19:21 1.9K rmsk.sql 2012-06-10 18:46 1.8K mrnaOrientInfo.sql 2020-08-20 21:22 1.8K estOrientInfo.sql 2016-06-19 05:25 1.8K hgFindSpec.sql 2021-12-17 16:13 1.8K snp138CodingDbSnp.sql 2014-03-02 03:40 1.7K xenoRefFlat.sql 2020-08-20 21:21 1.7K chainVicPac1.sql 2012-11-18 10:30 1.7K chainTurTru2.sql 2012-12-02 10:01 1.7K chainCerSim1.sql 2013-01-29 14:53 1.7K cpgIslandExtUnmasked.sql 2014-06-01 08:44 1.7K refFlat.sql 2020-08-20 21:21 1.7K chainSusScr2.sql 2012-06-10 15:22 1.6K chainOrnAna1.sql 2012-06-10 16:36 1.6K chainMonDom5.sql 2012-06-10 20:09 1.6K chainCanFam2.sql 2012-06-11 01:56 1.6K chainMm10.sql 2012-06-10 17:16 1.6K chainHg19.sql 2012-06-10 19:04 1.6K chainRn4.sql 2012-06-10 17:09 1.6K cpgIslandExt.sql 2012-06-10 18:59 1.6K genscan.sql 2012-06-11 04:40 1.6K gold.sql 2012-06-10 20:08 1.6K gbLoaded.sql 2020-08-20 21:41 1.6K tableList.sql 2022-10-02 03:11 1.6K chainVicPac1Link.sql 2012-11-18 10:13 1.6K chainTurTru2Link.sql 2012-12-02 10:09 1.6K chainCerSim1Link.sql 2013-01-29 14:44 1.6K gap.sql 2012-06-10 18:46 1.5K cytoBandIdeo.sql 2013-04-28 10:33 1.5K history.sql 2012-06-11 04:24 1.5K genscanSubopt.sql 2012-06-10 20:38 1.5K animalQtl.sql 2014-06-29 15:28 1.5K microsat.sql 2015-08-23 10:30 1.5K chainSusScr2Link.sql 2012-06-10 21:35 1.5K chainOrnAna1Link.sql 2012-06-11 01:25 1.5K chainMonDom5Link.sql 2012-06-11 02:03 1.5K chainCanFam2Link.sql 2012-06-11 03:22 1.5K ctgPos2.sql 2012-06-10 17:06 1.5K chainMm10Link.sql 2012-06-10 17:24 1.5K chainHg19Link.sql 2012-06-10 13:31 1.5K chainRn4Link.sql 2012-06-10 20:38 1.5K windowmaskerSdust.sql 2012-06-10 16:54 1.4K ucscToINSDC.sql 2013-09-15 08:53 1.4K chromAlias.sql 2016-09-15 17:55 1.4K tableDescriptions.sql 2020-10-10 02:03 1.4K snp138ExceptionDesc.sql 2014-03-02 03:38 1.4K bigFiles.sql 2022-10-02 03:11 1.4K grp.sql 2014-03-02 03:37 1.3K snp138Seq.sql 2014-03-02 03:37 1.3K chromInfo.sql 2012-06-10 20:27 1.3K gc5BaseBw.sql 2012-06-10 18:24 1.2K snp138ExceptionDesc.txt.gz 2014-03-02 03:38 1.0K hgFindSpec.txt.gz 2021-12-17 16:13 895 history.txt.gz 2012-06-11 04:24 705 grp.txt.gz 2014-03-02 03:37 208 bigFiles.txt.gz 2022-10-02 03:11 68 gc5BaseBw.txt.gz 2012-06-10 18:24 63