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