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