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.
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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 -
all_est.sql 19-Jun-2016 05:26 2.1K
all_est.txt.gz 19-Jun-2016 05:26 64M
all_mrna.sql 09-Jul-2017 07:43 2.1K
all_mrna.txt.gz 09-Jul-2017 07:43 1.6M
animalQtl.sql 29-Jun-2014 15:28 1.5K
animalQtl.txt.gz 29-Jun-2014 15:28 79K
augustusGene.sql 26-Jul-2015 10:20 1.9K
augustusGene.txt.gz 26-Jul-2015 10:20 2.4M
bigFiles.sql 16-Jul-2017 05:29 1.4K
bigFiles.txt.gz 16-Jul-2017 05:29 68
chainCanFam2.sql 11-Jun-2012 01:56 1.6K
chainCanFam2.txt.gz 11-Jun-2012 01:58 75M
chainCanFam2Link.sql 11-Jun-2012 03:22 1.5K
chainCanFam2Link.txt.gz 11-Jun-2012 03:37 681M
chainCerSim1.sql 29-Jan-2013 14:53 1.7K
chainCerSim1.txt.gz 29-Jan-2013 14:53 365M
chainCerSim1Link.sql 29-Jan-2013 14:44 1.6K
chainCerSim1Link.txt.gz 29-Jan-2013 14:47 1.6G
chainHg19.sql 10-Jun-2012 19:04 1.6K
chainHg19.txt.gz 10-Jun-2012 19:10 202M
chainHg19Link.sql 10-Jun-2012 13:31 1.5K
chainHg19Link.txt.gz 10-Jun-2012 13:52 907M
chainMm10.sql 10-Jun-2012 17:16 1.6K
chainMm10.txt.gz 10-Jun-2012 17:19 73M
chainMm10Link.sql 10-Jun-2012 17:24 1.5K
chainMm10Link.txt.gz 10-Jun-2012 17:39 530M
chainMonDom5.sql 10-Jun-2012 20:09 1.6K
chainMonDom5.txt.gz 10-Jun-2012 20:14 247M
chainMonDom5Link.sql 11-Jun-2012 02:03 1.5K
chainMonDom5Link.txt.gz 11-Jun-2012 02:18 763M
chainOrnAna1.sql 10-Jun-2012 16:36 1.6K
chainOrnAna1.txt.gz 10-Jun-2012 16:37 46M
chainOrnAna1Link.sql 11-Jun-2012 01:25 1.5K
chainOrnAna1Link.txt.gz 11-Jun-2012 01:31 257M
chainRn4.sql 10-Jun-2012 17:09 1.6K
chainRn4.txt.gz 10-Jun-2012 17:10 66M
chainRn4Link.sql 10-Jun-2012 20:38 1.5K
chainRn4Link.txt.gz 10-Jun-2012 20:47 508M
chainSusScr2.sql 10-Jun-2012 15:22 1.6K
chainSusScr2.txt.gz 10-Jun-2012 15:46 749M
chainSusScr2Link.sql 10-Jun-2012 21:35 1.5K
chainSusScr2Link.txt.gz 10-Jun-2012 22:42 3.1G
chainTurTru2.sql 02-Dec-2012 10:01 1.7K
chainTurTru2.txt.gz 02-Dec-2012 10:03 1.7G
chainTurTru2Link.sql 02-Dec-2012 10:09 1.6K
chainTurTru2Link.txt.gz 02-Dec-2012 10:15 4.3G
chainVicPac1.sql 18-Nov-2012 10:30 1.7K
chainVicPac1.txt.gz 18-Nov-2012 10:31 1.0G
chainVicPac1Link.sql 18-Nov-2012 10:13 1.6K
chainVicPac1Link.txt.gz 18-Nov-2012 10:18 3.1G
chromInfo.sql 10-Jun-2012 20:27 1.3K
chromInfo.txt.gz 10-Jun-2012 20:27 75K
cpgIslandExt.sql 10-Jun-2012 18:59 1.6K
cpgIslandExt.txt.gz 10-Jun-2012 18:59 824K
cpgIslandExtUnmasked.sql 01-Jun-2014 08:44 1.7K
cpgIslandExtUnmasked.txt.gz 01-Jun-2014 08:44 957K
ctgPos2.sql 10-Jun-2012 17:06 1.5K
ctgPos2.txt.gz 10-Jun-2012 17:06 28K
cytoBandIdeo.sql 28-Apr-2013 10:33 1.5K
cytoBandIdeo.txt.gz 28-Apr-2013 10:33 71K
estOrientInfo.sql 19-Jun-2016 05:25 1.8K
estOrientInfo.txt.gz 19-Jun-2016 05:25 20M
gap.sql 10-Jun-2012 18:46 1.5K
gap.txt.gz 10-Jun-2012 18:46 1.0M
gbLoaded.sql 09-Jul-2017 07:43 1.6K
gbLoaded.txt.gz 09-Jul-2017 07:43 17K
gc5BaseBw.sql 10-Jun-2012 18:24 1.2K
gc5BaseBw.txt.gz 10-Jun-2012 18:24 63
genscan.sql 11-Jun-2012 04:40 1.6K
genscan.txt.gz 11-Jun-2012 04:40 3.1M
genscanSubopt.sql 10-Jun-2012 20:38 1.5K
genscanSubopt.txt.gz 10-Jun-2012 20:38 6.1M
gold.sql 10-Jun-2012 20:08 1.6K
gold.txt.gz 10-Jun-2012 20:08 2.4M
grp.sql 02-Mar-2014 03:37 1.3K
grp.txt.gz 02-Mar-2014 03:37 208
hgFindSpec.sql 16-Jul-2017 05:29 1.7K
hgFindSpec.txt.gz 16-Jul-2017 05:29 822
history.sql 11-Jun-2012 04:24 1.5K
history.txt.gz 11-Jun-2012 04:24 705
intronEst.sql 19-Jun-2016 05:25 2.1K
intronEst.txt.gz 19-Jun-2016 05:25 38M
microsat.sql 23-Aug-2015 10:30 1.5K
microsat.txt.gz 23-Aug-2015 10:30 313K
mrnaOrientInfo.sql 09-Jul-2017 07:43 1.8K
mrnaOrientInfo.txt.gz 09-Jul-2017 07:43 585K
nestedRepeats.sql 11-Jun-2012 02:02 1.9K
nestedRepeats.txt.gz 11-Jun-2012 02:02 16M
netCanFam2.sql 10-Jun-2012 16:41 2.0K
netCanFam2.txt.gz 10-Jun-2012 16:45 74M
netCerSim1.sql 29-Jan-2013 14:43 2.1K
netCerSim1.txt.gz 29-Jan-2013 14:44 67M
netHg19.sql 11-Jun-2012 01:49 2.0K
netHg19.txt.gz 11-Jun-2012 01:51 68M
netMm10.sql 10-Jun-2012 21:30 2.0K
netMm10.txt.gz 10-Jun-2012 21:33 56M
netMonDom5.sql 10-Jun-2012 18:24 2.0K
netMonDom5.txt.gz 10-Jun-2012 18:25 18M
netOrnAna1.sql 11-Jun-2012 03:20 2.0K
netOrnAna1.txt.gz 11-Jun-2012 03:21 18M
netRn4.sql 10-Jun-2012 21:24 2.0K
netRn4.txt.gz 10-Jun-2012 21:26 54M
netSusScr2.sql 11-Jun-2012 03:11 2.0K
netSusScr2.txt.gz 11-Jun-2012 03:13 66M
netTurTru2.sql 02-Dec-2012 10:08 2.1K
netTurTru2.txt.gz 02-Dec-2012 10:08 67M
netVicPac1.sql 18-Nov-2012 10:34 2.1K
netVicPac1.txt.gz 18-Nov-2012 10:34 66M
pubsBingBlat.sql 26-Jan-2014 08:18 2.4K
pubsBingBlat.txt.gz 26-Jan-2014 08:18 3.2M
pubsBingBlatPsl.sql 26-Jan-2014 08:18 2.2K
pubsBingBlatPsl.txt.gz 26-Jan-2014 08:18 2.1M
refFlat.sql 09-Jul-2017 07:42 1.7K
refFlat.txt.gz 09-Jul-2017 07:42 1.4M
refGene.sql 09-Jul-2017 07:43 1.9K
refGene.txt.gz 09-Jul-2017 07:43 1.5M
refSeqAli.sql 09-Jul-2017 07:43 2.1K
refSeqAli.txt.gz 09-Jul-2017 07:43 1.5M
rmsk.sql 10-Jun-2012 18:46 1.8K
rmsk.txt.gz 10-Jun-2012 18:50 144M
simpleRepeat.sql 10-Jun-2012 19:21 1.9K
simpleRepeat.txt.gz 10-Jun-2012 19:21 13M
snp138.sql 02-Mar-2014 03:38 3.0K
snp138.txt.gz 02-Mar-2014 03:39 338M
snp138CodingDbSnp.sql 02-Mar-2014 03:40 1.7K
snp138CodingDbSnp.txt.gz 02-Mar-2014 03:40 2.1M
snp138Common.sql 02-Mar-2014 03:40 3.0K
snp138Common.txt.gz 02-Mar-2014 03:40 395K
snp138ExceptionDesc.sql 02-Mar-2014 03:38 1.4K
snp138ExceptionDesc.txt.gz 02-Mar-2014 03:38 1.0K
snp138Mult.sql 02-Mar-2014 03:40 3.0K
snp138Mult.txt.gz 02-Mar-2014 03:40 40M
snp138Seq.sql 02-Mar-2014 03:37 1.3K
snp138Seq.txt.gz 02-Mar-2014 03:37 136M
tableDescriptions.sql 16-Jul-2017 05:29 1.4K
tableDescriptions.txt.gz 16-Jul-2017 05:29 7.0K
tableList.sql 16-Jul-2017 05:29 1.5K
tableList.txt.gz 16-Jul-2017 05:29 5.0K
trackDb.sql 16-Jul-2017 05:29 2.0K
trackDb.txt.gz 16-Jul-2017 05:29 56K
ucscToINSDC.sql 15-Sep-2013 08:53 1.4K
ucscToINSDC.txt.gz 15-Sep-2013 08:53 97K
windowmaskerSdust.sql 10-Jun-2012 16:54 1.4K
windowmaskerSdust.txt.gz 10-Jun-2012 16:58 121M
xenoMrna.sql 09-Jul-2017 07:39 2.1K
xenoMrna.txt.gz 09-Jul-2017 07:41 285M
xenoRefFlat.sql 09-Jul-2017 07:42 1.7K
xenoRefFlat.txt.gz 09-Jul-2017 07:42 25M
xenoRefGene.sql 09-Jul-2017 07:43 1.9K
xenoRefGene.txt.gz 09-Jul-2017 07:43 27M
xenoRefSeqAli.sql 09-Jul-2017 07:43 2.1K
xenoRefSeqAli.txt.gz 09-Jul-2017 07:43 24M