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 -
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 2.0K
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 2024-07-25 09:34 75K
trackDb.sql 2024-07-25 09:34 2.1K
tableList.txt.gz 2024-11-17 03:38 5.1K
tableList.sql 2024-11-17 03:38 1.6K
tableDescriptions.txt.gz 2024-11-16 02:03 8.2K
tableDescriptions.sql 2024-11-16 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 2024-07-25 09:34 1.0K
hgFindSpec.sql 2024-07-25 09:34 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 2024-11-17 03:38 68
bigFiles.sql 2024-11-17 03:38 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