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 -
chainHg19Link.sql 2012-06-10 13:31 1.5K
chainHg19Link.txt.gz 2012-06-10 13:52 907M
chainSusScr2.sql 2012-06-10 15:22 1.6K
chainSusScr2.txt.gz 2012-06-10 15:46 749M
chainOrnAna1.sql 2012-06-10 16:36 1.6K
chainOrnAna1.txt.gz 2012-06-10 16:37 46M
netCanFam2.sql 2012-06-10 16:41 2.0K
netCanFam2.txt.gz 2012-06-10 16:45 74M
windowmaskerSdust.sql 2012-06-10 16:54 1.4K
windowmaskerSdust.txt.gz 2012-06-10 16:58 121M
ctgPos2.sql 2012-06-10 17:06 1.5K
ctgPos2.txt.gz 2012-06-10 17:06 28K
chainRn4.sql 2012-06-10 17:09 1.6K
chainRn4.txt.gz 2012-06-10 17:10 66M
chainMm10.sql 2012-06-10 17:16 1.6K
chainMm10.txt.gz 2012-06-10 17:19 73M
chainMm10Link.sql 2012-06-10 17:24 1.5K
chainMm10Link.txt.gz 2012-06-10 17:39 530M
gc5BaseBw.sql 2012-06-10 18:24 1.2K
gc5BaseBw.txt.gz 2012-06-10 18:24 63
netMonDom5.sql 2012-06-10 18:24 2.0K
netMonDom5.txt.gz 2012-06-10 18:25 18M
gap.sql 2012-06-10 18:46 1.5K
gap.txt.gz 2012-06-10 18:46 1.0M
rmsk.sql 2012-06-10 18:46 1.8K
rmsk.txt.gz 2012-06-10 18:50 144M
cpgIslandExt.sql 2012-06-10 18:59 1.6K
cpgIslandExt.txt.gz 2012-06-10 18:59 824K
chainHg19.sql 2012-06-10 19:04 1.6K
chainHg19.txt.gz 2012-06-10 19:10 202M
simpleRepeat.sql 2012-06-10 19:21 1.9K
simpleRepeat.txt.gz 2012-06-10 19:21 13M
gold.sql 2012-06-10 20:08 1.6K
gold.txt.gz 2012-06-10 20:08 2.4M
chainMonDom5.sql 2012-06-10 20:09 1.6K
chainMonDom5.txt.gz 2012-06-10 20:14 247M
chromInfo.sql 2012-06-10 20:27 1.3K
chromInfo.txt.gz 2012-06-10 20:27 75K
genscanSubopt.sql 2012-06-10 20:38 1.5K
genscanSubopt.txt.gz 2012-06-10 20:38 6.1M
chainRn4Link.sql 2012-06-10 20:38 1.5K
chainRn4Link.txt.gz 2012-06-10 20:47 508M
netRn4.sql 2012-06-10 21:24 2.0K
netRn4.txt.gz 2012-06-10 21:26 54M
netMm10.sql 2012-06-10 21:30 2.0K
netMm10.txt.gz 2012-06-10 21:33 56M
chainSusScr2Link.sql 2012-06-10 21:35 1.5K
chainSusScr2Link.txt.gz 2012-06-10 22:42 3.1G
chainOrnAna1Link.sql 2012-06-11 01:25 1.5K
chainOrnAna1Link.txt.gz 2012-06-11 01:31 257M
netHg19.sql 2012-06-11 01:49 2.0K
netHg19.txt.gz 2012-06-11 01:51 68M
chainCanFam2.sql 2012-06-11 01:56 1.6K
chainCanFam2.txt.gz 2012-06-11 01:58 75M
nestedRepeats.sql 2012-06-11 02:02 1.9K
nestedRepeats.txt.gz 2012-06-11 02:02 16M
chainMonDom5Link.sql 2012-06-11 02:03 1.5K
chainMonDom5Link.txt.gz 2012-06-11 02:18 763M
netSusScr2.sql 2012-06-11 03:11 2.0K
netSusScr2.txt.gz 2012-06-11 03:13 66M
netOrnAna1.sql 2012-06-11 03:20 2.0K
netOrnAna1.txt.gz 2012-06-11 03:21 18M
chainCanFam2Link.sql 2012-06-11 03:22 1.5K
chainCanFam2Link.txt.gz 2012-06-11 03:37 681M
history.sql 2012-06-11 04:24 1.5K
history.txt.gz 2012-06-11 04:24 705
genscan.sql 2012-06-11 04:40 1.6K
genscan.txt.gz 2012-06-11 04:40 3.1M
chainVicPac1Link.sql 2012-11-18 10:13 1.6K
chainVicPac1Link.txt.gz 2012-11-18 10:18 3.1G
chainVicPac1.sql 2012-11-18 10:30 1.7K
chainVicPac1.txt.gz 2012-11-18 10:31 1.0G
netVicPac1.sql 2012-11-18 10:34 2.1K
netVicPac1.txt.gz 2012-11-18 10:34 66M
chainTurTru2.sql 2012-12-02 10:01 1.7K
chainTurTru2.txt.gz 2012-12-02 10:03 1.7G
netTurTru2.sql 2012-12-02 10:08 2.1K
netTurTru2.txt.gz 2012-12-02 10:08 67M
chainTurTru2Link.sql 2012-12-02 10:09 1.6K
chainTurTru2Link.txt.gz 2012-12-02 10:15 4.3G
netCerSim1.sql 2013-01-29 14:43 2.1K
netCerSim1.txt.gz 2013-01-29 14:44 67M
chainCerSim1Link.sql 2013-01-29 14:44 1.6K
chainCerSim1Link.txt.gz 2013-01-29 14:47 1.6G
chainCerSim1.sql 2013-01-29 14:53 1.7K
chainCerSim1.txt.gz 2013-01-29 14:53 365M
cytoBandIdeo.sql 2013-04-28 10:33 1.5K
cytoBandIdeo.txt.gz 2013-04-28 10:33 71K
ucscToINSDC.sql 2013-09-15 08:53 1.4K
ucscToINSDC.txt.gz 2013-09-15 08:53 97K
pubsBingBlat.sql 2014-01-26 08:18 2.4K
pubsBingBlat.txt.gz 2014-01-26 08:18 3.2M
pubsBingBlatPsl.sql 2014-01-26 08:18 2.2K
pubsBingBlatPsl.txt.gz 2014-01-26 08:18 2.1M
grp.sql 2014-03-02 03:37 1.3K
grp.txt.gz 2014-03-02 03:37 208
snp138Seq.sql 2014-03-02 03:37 1.3K
snp138Seq.txt.gz 2014-03-02 03:37 136M
snp138.sql 2014-03-02 03:38 3.0K
snp138ExceptionDesc.sql 2014-03-02 03:38 1.4K
snp138ExceptionDesc.txt.gz 2014-03-02 03:38 1.0K
snp138.txt.gz 2014-03-02 03:39 338M
snp138CodingDbSnp.sql 2014-03-02 03:40 1.7K
snp138CodingDbSnp.txt.gz 2014-03-02 03:40 2.1M
snp138Mult.sql 2014-03-02 03:40 3.0K
snp138Mult.txt.gz 2014-03-02 03:40 40M
snp138Common.sql 2014-03-02 03:40 3.0K
snp138Common.txt.gz 2014-03-02 03:40 395K
cpgIslandExtUnmasked.sql 2014-06-01 08:44 1.7K
cpgIslandExtUnmasked.txt.gz 2014-06-01 08:44 957K
animalQtl.sql 2014-06-29 15:28 1.5K
animalQtl.txt.gz 2014-06-29 15:28 79K
augustusGene.sql 2015-07-26 10:20 1.9K
augustusGene.txt.gz 2015-07-26 10:20 2.4M
microsat.sql 2015-08-23 10:30 1.5K
microsat.txt.gz 2015-08-23 10:30 313K
intronEst.sql 2016-06-19 05:25 2.1K
intronEst.txt.gz 2016-06-19 05:25 38M
estOrientInfo.sql 2016-06-19 05:25 1.8K
estOrientInfo.txt.gz 2016-06-19 05:25 20M
all_est.sql 2016-06-19 05:26 2.1K
all_est.txt.gz 2016-06-19 05:26 64M
chromAlias.sql 2016-09-15 17:55 1.4K
chromAlias.txt.gz 2016-09-15 17:55 70K
all_mrna.sql 2020-08-20 21:06 2.1K
all_mrna.txt.gz 2020-08-20 21:06 1.6M
xenoMrna.sql 2020-08-20 21:06 2.1K
xenoMrna.txt.gz 2020-08-20 21:06 313M
refGene.sql 2020-08-20 21:21 1.9K
refGene.txt.gz 2020-08-20 21:21 1.5M
refFlat.sql 2020-08-20 21:21 1.7K
refFlat.txt.gz 2020-08-20 21:21 1.4M
xenoRefGene.sql 2020-08-20 21:21 2.0K
xenoRefGene.txt.gz 2020-08-20 21:21 33M
xenoRefFlat.sql 2020-08-20 21:21 1.7K
xenoRefFlat.txt.gz 2020-08-20 21:21 29M
mrnaOrientInfo.sql 2020-08-20 21:22 1.8K
mrnaOrientInfo.txt.gz 2020-08-20 21:22 598K
refSeqAli.sql 2020-08-20 21:26 2.1K
refSeqAli.txt.gz 2020-08-20 21:26 1.5M
xenoRefSeqAli.sql 2020-08-20 21:26 2.1K
xenoRefSeqAli.txt.gz 2020-08-20 21:26 32M
gbLoaded.sql 2020-08-20 21:41 1.6K
gbLoaded.txt.gz 2020-08-20 21:41 45K
trackDb_pushedout.sql 2023-09-18 17:06 2.1K
trackDb_pushedout.txt.gz 2023-09-18 17:06 64K
hgFindSpec_pushedout.sql 2023-09-18 17:06 1.8K
hgFindSpec_pushedout.txt.gz 2023-09-18 17:06 1.0K
trackDb.sql 2023-09-19 16:08 2.1K
trackDb.txt.gz 2023-09-19 16:08 64K
hgFindSpec.sql 2023-09-19 16:08 1.8K
hgFindSpec.txt.gz 2023-09-19 16:08 1.0K
tableDescriptions.sql 2024-04-20 02:03 1.5K
tableDescriptions.txt.gz 2024-04-20 02:03 8.2K
tableList.sql 2024-04-21 03:37 1.6K
tableList.txt.gz 2024-04-21 03:37 5.2K
bigFiles.sql 2024-04-21 03:37 1.4K
bigFiles.txt.gz 2024-04-21 03:37 68