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