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 -
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
trackDb.txt.gz 2024-07-25 09:34 75K
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
gbLoaded.txt.gz 2020-08-20 21:41 45K
ctgPos2.txt.gz 2012-06-10 17:06 28K
tableDescriptions.txt.gz 2024-11-16 02:03 8.2K
tableList.txt.gz 2024-11-17 03:38 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
xenoMrna.sql 2020-08-20 21:06 2.1K
all_mrna.sql 2020-08-20 21:06 2.1K
intronEst.sql 2016-06-19 05:25 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 2024-07-25 09:34 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
xenoRefGene.sql 2020-08-20 21:21 2.0K
refGene.sql 2020-08-20 21:21 1.9K
augustusGene.sql 2015-07-26 10:20 1.9K
nestedRepeats.sql 2012-06-11 02:02 1.9K
simpleRepeat.sql 2012-06-10 19:21 1.9K
mrnaOrientInfo.sql 2020-08-20 21:22 1.8K
rmsk.sql 2012-06-10 18:46 1.8K
estOrientInfo.sql 2016-06-19 05:25 1.8K
hgFindSpec.sql 2024-07-25 09:34 1.8K
xenoRefFlat.sql 2020-08-20 21:21 1.7K
snp138CodingDbSnp.sql 2014-03-02 03:40 1.7K
refFlat.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
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
gbLoaded.sql 2020-08-20 21:41 1.6K
gold.sql 2012-06-10 20:08 1.6K
tableList.sql 2024-11-17 03:38 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
chromAlias.sql 2016-09-15 17:55 1.4K
windowmaskerSdust.sql 2012-06-10 16:54 1.4K
ucscToINSDC.sql 2013-09-15 08:53 1.4K
tableDescriptions.sql 2024-11-16 02:03 1.4K
snp138ExceptionDesc.sql 2014-03-02 03:38 1.4K
bigFiles.sql 2024-11-17 03:38 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 2024-07-25 09:34 1.0K
history.txt.gz 2012-06-11 04:24 705
grp.txt.gz 2014-03-02 03:37 208
bigFiles.txt.gz 2024-11-17 03:38 68
gc5BaseBw.txt.gz 2012-06-10 18:24 63