This directory contains a dump of the UCSC genome annotation database for
the Nov. 2009 (Bos_taurus_UMD_3.1/bosTau6) assembly of the cow genome (bosTau6, UMD_3.1 (NCBI project 10708, accession GCA_000003055.3)).
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/sites/entrez?Db=genomeprj&cmd=ShowDetailView&TermToSearch=10708
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=bosTau6
and click the "describe table schema" button. There is also a "view
table schema" link on the configuration page for each track.
---------------------------------------------------------------
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/bosTau6/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/bosTau6/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/bosTau6/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/bosTau6/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/bosTau6/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 bosTau6 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql bosTau6 --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 -
chainHg19.sql 2011-11-02 11:01 1.6K
chainHg19.txt.gz 2011-11-02 11:02 180M
chainMm9.sql 2011-11-02 11:05 1.6K
chainMm9.txt.gz 2011-11-02 11:06 64M
chainOrnAna1.sql 2011-11-02 11:07 1.6K
chainOrnAna1.txt.gz 2011-11-02 11:07 41M
chainSusScr2.sql 2011-11-02 11:08 1.6K
chainSusScr2.txt.gz 2011-11-02 11:24 1.4G
chainMonDom5Link.sql 2011-11-02 11:46 1.5K
chainMonDom5Link.txt.gz 2011-11-02 11:50 656M
netCanFam2.sql 2011-11-02 12:11 2.0K
netCanFam2.txt.gz 2011-11-02 12:12 71M
gc5BaseBw.sql 2011-11-02 12:13 1.2K
gc5BaseBw.txt.gz 2011-11-02 12:13 63
chainCanFam2Link.sql 2011-11-02 12:13 1.5K
chainCanFam2Link.txt.gz 2011-11-02 12:18 650M
ucscToEnsembl.sql 2011-11-02 12:36 1.3K
ucscToEnsembl.txt.gz 2011-11-02 12:36 19K
nestedRepeats.sql 2011-11-02 12:36 1.9K
nestedRepeats.txt.gz 2011-11-02 12:36 15M
chainSusScr2Link.sql 2011-11-02 12:36 1.5K
chainSusScr2Link.txt.gz 2011-11-02 13:33 6.9G
cpgIslandExt.sql 2011-11-02 15:09 1.6K
cpgIslandExt.txt.gz 2011-11-02 15:09 811K
simpleRepeat.sql 2011-11-02 15:09 1.9K
simpleRepeat.txt.gz 2011-11-02 15:09 12M
netHg19.sql 2011-11-02 15:09 2.0K
netHg19.txt.gz 2011-11-02 15:09 66M
chainOrnAna1Link.sql 2011-11-02 15:10 1.5K
chainOrnAna1Link.txt.gz 2011-11-02 15:11 234M
rmsk.sql 2011-11-02 15:15 1.8K
rmsk.txt.gz 2011-11-02 15:15 135M
netMm9.sql 2011-11-02 15:17 2.0K
netMm9.txt.gz 2011-11-02 15:18 54M
netMonDom5.sql 2011-11-02 15:19 2.0K
netMonDom5.txt.gz 2011-11-02 15:19 17M
history.sql 2011-11-02 15:21 1.5K
history.txt.gz 2011-11-02 15:21 608
gap.sql 2011-11-02 15:21 1.5K
gap.txt.gz 2011-11-02 15:21 1.0M
chainHg19Link.sql 2011-11-02 15:21 1.5K
chainHg19Link.txt.gz 2011-11-02 15:26 835M
ctgPos2.sql 2011-11-02 15:38 1.5K
ctgPos2.txt.gz 2011-11-02 15:38 47K
chainRn4.sql 2011-11-02 15:38 1.6K
chainRn4.txt.gz 2011-11-02 15:39 55M
chainMonDom5.sql 2011-11-02 15:39 1.6K
chainMonDom5.txt.gz 2011-11-02 15:40 210M
chainRn4Link.sql 2011-11-02 15:43 1.5K
chainRn4Link.txt.gz 2011-11-02 15:46 455M
gold.sql 2011-11-02 15:52 1.6K
gold.txt.gz 2011-11-02 15:52 1.3M
chainMm9Link.sql 2011-11-02 15:56 1.5K
chainMm9Link.txt.gz 2011-11-02 15:59 491M
netRn4.sql 2011-11-02 16:07 2.0K
netRn4.txt.gz 2011-11-02 16:08 52M
netOrnAna1.sql 2011-11-02 16:08 2.0K
netOrnAna1.txt.gz 2011-11-02 16:08 17M
netSusScr2.sql 2011-11-02 16:08 2.0K
netSusScr2.txt.gz 2011-11-02 16:09 65M
chainCanFam2.sql 2011-11-02 16:10 1.6K
chainCanFam2.txt.gz 2011-11-02 16:10 71M
chromInfo.sql 2011-11-02 16:11 1.3K
chromInfo.txt.gz 2011-11-02 16:11 16K
tRNAs.sql 2012-04-15 15:40 1.7K
tRNAs.txt.gz 2012-04-15 15:40 107K
cytoBandIdeo.sql 2013-08-11 03:45 1.5K
cytoBandIdeo.txt.gz 2013-08-11 03:45 16K
bamAllNumtSSorted.sql 2013-08-18 03:44 1.3K
bamAllNumtSSorted.txt.gz 2013-08-18 03:44 85
numtS.sql 2013-08-18 03:44 1.7K
numtS.txt.gz 2013-08-18 03:44 8.8K
numtSAssembled.sql 2013-08-18 03:44 1.8K
numtSAssembled.txt.gz 2013-08-18 03:44 2.7K
numtSMitochondrion.sql 2013-08-18 03:44 1.6K
numtSMitochondrion.txt.gz 2013-08-18 03:44 2.4K
grp.sql 2014-03-02 03:37 1.3K
grp.txt.gz 2014-03-02 03:37 208
cpgIslandExtUnmasked.sql 2014-06-01 08:38 1.7K
cpgIslandExtUnmasked.txt.gz 2014-06-01 08:38 924K
augustusGene.sql 2015-07-26 10:13 1.9K
augustusGene.txt.gz 2015-07-26 10:13 2.3M
microsat.sql 2015-08-23 10:22 1.5K
microsat.txt.gz 2015-08-23 10:22 275K
all_est.sql 2016-06-19 05:20 2.1K
all_est.txt.gz 2016-06-19 05:20 62M
estOrientInfo.sql 2016-06-19 05:20 1.8K
estOrientInfo.txt.gz 2016-06-19 05:20 19M
intronEst.sql 2016-06-19 05:20 2.1K
intronEst.txt.gz 2016-06-19 05:21 37M
ensGtp.sql 2018-08-05 05:24 1.4K
ensGtp.txt.gz 2018-08-05 05:24 311K
ensPep.sql 2018-08-05 05:24 1.3K
ensPep.txt.gz 2018-08-05 05:24 6.7M
ensemblSource.sql 2018-08-05 05:24 1.4K
ensemblSource.txt.gz 2018-08-05 05:24 86K
ensGene.sql 2018-08-05 05:27 1.9K
ensGene.txt.gz 2018-08-05 05:27 2.3M
chromAlias.sql 2018-08-05 05:27 1.4K
chromAlias.txt.gz 2018-08-05 05:27 14K
ensemblToGeneName.sql 2018-08-05 05:27 1.4K
ensemblToGeneName.txt.gz 2018-08-05 05:27 168K
all_mrna.sql 2020-08-20 21:43 2.1K
all_mrna.txt.gz 2020-08-20 21:43 1.6M
xenoMrna.sql 2020-08-20 21:43 2.1K
xenoMrna.txt.gz 2020-08-20 21:43 346M
refGene.sql 2020-08-20 21:48 1.9K
refGene.txt.gz 2020-08-20 21:48 1.5M
refFlat.sql 2020-08-20 21:48 1.7K
refFlat.txt.gz 2020-08-20 21:48 1.4M
xenoRefGene.sql 2020-08-20 21:48 2.0K
xenoRefGene.txt.gz 2020-08-20 21:48 32M
xenoRefFlat.sql 2020-08-20 21:48 1.7K
xenoRefFlat.txt.gz 2020-08-20 21:48 29M
mrnaOrientInfo.sql 2020-08-20 21:48 1.8K
mrnaOrientInfo.txt.gz 2020-08-20 21:48 595K
refSeqAli.sql 2020-08-20 21:48 2.1K
refSeqAli.txt.gz 2020-08-20 21:48 1.5M
xenoRefSeqAli.sql 2020-08-20 21:48 2.1K
xenoRefSeqAli.txt.gz 2020-08-20 21:48 34M
gbLoaded.sql 2020-08-20 21:48 1.6K
gbLoaded.txt.gz 2020-08-20 21:48 107K
trackDb_pushedout.sql 2023-09-18 17:06 2.1K
trackDb_pushedout.txt.gz 2023-09-18 17:06 42K
hgFindSpec_pushedout.sql 2023-09-18 17:06 1.8K
hgFindSpec_pushedout.txt.gz 2023-09-18 17:06 931
trackDb.sql 2023-09-19 16:08 2.1K
trackDb.txt.gz 2023-09-19 16:08 42K
hgFindSpec.sql 2023-09-19 16:08 1.8K
hgFindSpec.txt.gz 2023-09-19 16:08 921
tableDescriptions.sql 2024-04-20 02:03 1.5K
tableDescriptions.txt.gz 2024-04-20 02:03 6.3K
tableList.sql 2024-04-21 03:36 1.6K
tableList.txt.gz 2024-04-21 03:36 3.8K
bigFiles.sql 2024-04-21 03:36 1.4K
bigFiles.txt.gz 2024-04-21 03:36 109