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.
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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/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 -
chainSusScr2Link.txt.gz 2011-11-02 13:33 6.9G
chainSusScr2.txt.gz 2011-11-02 11:24 1.4G
chainHg19Link.txt.gz 2011-11-02 15:26 835M
chainMonDom5Link.txt.gz 2011-11-02 11:50 656M
chainCanFam2Link.txt.gz 2011-11-02 12:18 650M
chainMm9Link.txt.gz 2011-11-02 15:59 491M
chainRn4Link.txt.gz 2011-11-02 15:46 455M
xenoMrna.txt.gz 2020-08-20 21:43 346M
chainOrnAna1Link.txt.gz 2011-11-02 15:11 234M
chainMonDom5.txt.gz 2011-11-02 15:40 210M
chainHg19.txt.gz 2011-11-02 11:02 180M
rmsk.txt.gz 2011-11-02 15:15 135M
chainCanFam2.txt.gz 2011-11-02 16:10 71M
netCanFam2.txt.gz 2011-11-02 12:12 71M
netHg19.txt.gz 2011-11-02 15:09 66M
netSusScr2.txt.gz 2011-11-02 16:09 65M
chainMm9.txt.gz 2011-11-02 11:06 64M
all_est.txt.gz 2016-06-19 05:20 62M
chainRn4.txt.gz 2011-11-02 15:39 55M
netMm9.txt.gz 2011-11-02 15:18 54M
netRn4.txt.gz 2011-11-02 16:08 52M
chainOrnAna1.txt.gz 2011-11-02 11:07 41M
intronEst.txt.gz 2016-06-19 05:21 37M
xenoRefSeqAli.txt.gz 2020-08-20 21:48 34M
xenoRefGene.txt.gz 2020-08-20 21:48 32M
xenoRefFlat.txt.gz 2020-08-20 21:48 29M
estOrientInfo.txt.gz 2016-06-19 05:20 19M
netOrnAna1.txt.gz 2011-11-02 16:08 17M
netMonDom5.txt.gz 2011-11-02 15:19 17M
nestedRepeats.txt.gz 2011-11-02 12:36 15M
simpleRepeat.txt.gz 2011-11-02 15:09 12M
ensPep.txt.gz 2018-08-05 05:24 6.7M
augustusGene.txt.gz 2015-07-26 10:13 2.3M
ensGene.txt.gz 2018-08-05 05:27 2.3M
all_mrna.txt.gz 2020-08-20 21:43 1.6M
refSeqAli.txt.gz 2020-08-20 21:48 1.5M
refGene.txt.gz 2020-08-20 21:48 1.5M
refFlat.txt.gz 2020-08-20 21:48 1.4M
gold.txt.gz 2011-11-02 15:52 1.3M
gap.txt.gz 2011-11-02 15:21 1.0M
cpgIslandExtUnmasked.txt.gz 2014-06-01 08:38 924K
cpgIslandExt.txt.gz 2011-11-02 15:09 811K
mrnaOrientInfo.txt.gz 2020-08-20 21:48 595K
ensGtp.txt.gz 2018-08-05 05:24 311K
microsat.txt.gz 2015-08-23 10:22 275K
ensemblToGeneName.txt.gz 2018-08-05 05:27 168K
gbLoaded.txt.gz 2020-08-20 21:48 107K
tRNAs.txt.gz 2012-04-15 15:40 107K
ensemblSource.txt.gz 2018-08-05 05:24 86K
ctgPos2.txt.gz 2011-11-02 15:38 47K
trackDb.txt.gz 2023-09-19 16:08 42K
ucscToEnsembl.txt.gz 2011-11-02 12:36 19K
cytoBandIdeo.txt.gz 2013-08-11 03:45 16K
chromInfo.txt.gz 2011-11-02 16:11 16K
chromAlias.txt.gz 2018-08-05 05:27 14K
numtS.txt.gz 2013-08-18 03:44 8.8K
tableDescriptions.txt.gz 2024-11-23 02:03 6.3K
tableList.txt.gz 2024-11-24 03:31 3.6K
numtSAssembled.txt.gz 2013-08-18 03:44 2.7K
numtSMitochondrion.txt.gz 2013-08-18 03:44 2.4K
xenoRefSeqAli.sql 2020-08-20 21:48 2.1K
refSeqAli.sql 2020-08-20 21:48 2.1K
xenoMrna.sql 2020-08-20 21:43 2.1K
all_mrna.sql 2020-08-20 21:43 2.1K
intronEst.sql 2016-06-19 05:20 2.1K
all_est.sql 2016-06-19 05:20 2.1K
trackDb.sql 2023-09-19 16:08 2.1K
netSusScr2.sql 2011-11-02 16:08 2.0K
netOrnAna1.sql 2011-11-02 16:08 2.0K
netMonDom5.sql 2011-11-02 15:19 2.0K
netCanFam2.sql 2011-11-02 12:11 2.0K
netHg19.sql 2011-11-02 15:09 2.0K
netRn4.sql 2011-11-02 16:07 2.0K
netMm9.sql 2011-11-02 15:17 2.0K
xenoRefGene.sql 2020-08-20 21:48 2.0K
refGene.sql 2020-08-20 21:48 1.9K
augustusGene.sql 2015-07-26 10:13 1.9K
ensGene.sql 2018-08-05 05:27 1.9K
nestedRepeats.sql 2011-11-02 12:36 1.9K
simpleRepeat.sql 2011-11-02 15:09 1.9K
numtSAssembled.sql 2013-08-18 03:44 1.8K
mrnaOrientInfo.sql 2020-08-20 21:48 1.8K
rmsk.sql 2011-11-02 15:15 1.8K
estOrientInfo.sql 2016-06-19 05:20 1.8K
hgFindSpec.sql 2023-09-19 16:08 1.8K
xenoRefFlat.sql 2020-08-20 21:48 1.7K
numtS.sql 2013-08-18 03:44 1.7K
refFlat.sql 2020-08-20 21:48 1.7K
cpgIslandExtUnmasked.sql 2014-06-01 08:38 1.7K
tRNAs.sql 2012-04-15 15:40 1.7K
chainSusScr2.sql 2011-11-02 11:08 1.6K
chainOrnAna1.sql 2011-11-02 11:07 1.6K
chainMonDom5.sql 2011-11-02 15:39 1.6K
chainCanFam2.sql 2011-11-02 16:10 1.6K
chainHg19.sql 2011-11-02 11:01 1.6K
chainRn4.sql 2011-11-02 15:38 1.6K
chainMm9.sql 2011-11-02 11:05 1.6K
cpgIslandExt.sql 2011-11-02 15:09 1.6K
gbLoaded.sql 2020-08-20 21:48 1.6K
gold.sql 2011-11-02 15:52 1.6K
tableList.sql 2024-11-24 03:31 1.6K
numtSMitochondrion.sql 2013-08-18 03:44 1.6K
gap.sql 2011-11-02 15:21 1.5K
cytoBandIdeo.sql 2013-08-11 03:45 1.5K
history.sql 2011-11-02 15:21 1.5K
microsat.sql 2015-08-23 10:22 1.5K
chainSusScr2Link.sql 2011-11-02 12:36 1.5K
chainOrnAna1Link.sql 2011-11-02 15:10 1.5K
chainMonDom5Link.sql 2011-11-02 11:46 1.5K
chainCanFam2Link.sql 2011-11-02 12:13 1.5K
ctgPos2.sql 2011-11-02 15:38 1.5K
chainHg19Link.sql 2011-11-02 15:21 1.5K
chainRn4Link.sql 2011-11-02 15:43 1.5K
chainMm9Link.sql 2011-11-02 15:56 1.5K
tableDescriptions.sql 2024-11-23 02:03 1.5K
chromAlias.sql 2018-08-05 05:27 1.4K
ensGtp.sql 2018-08-05 05:24 1.4K
bigFiles.sql 2024-11-24 03:31 1.4K
ensemblToGeneName.sql 2018-08-05 05:27 1.4K
ensemblSource.sql 2018-08-05 05:24 1.4K
grp.sql 2014-03-02 03:37 1.3K
ensPep.sql 2018-08-05 05:24 1.3K
chromInfo.sql 2011-11-02 16:11 1.3K
bamAllNumtSSorted.sql 2013-08-18 03:44 1.3K
ucscToEnsembl.sql 2011-11-02 12:36 1.3K
gc5BaseBw.sql 2011-11-02 12:13 1.2K
hgFindSpec.txt.gz 2023-09-19 16:08 921
history.txt.gz 2011-11-02 15:21 608
grp.txt.gz 2014-03-02 03:37 208
bigFiles.txt.gz 2024-11-24 03:31 109
bamAllNumtSSorted.txt.gz 2013-08-18 03:44 85
gc5BaseBw.txt.gz 2011-11-02 12:13 63