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