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 -
all_est.sql 19-Jun-2016 05:20 2.1K
all_est.txt.gz 19-Jun-2016 05:20 62M
all_mrna.sql 09-Jul-2017 07:38 2.1K
all_mrna.txt.gz 09-Jul-2017 07:38 1.6M
augustusGene.sql 26-Jul-2015 10:13 1.9K
augustusGene.txt.gz 26-Jul-2015 10:13 2.3M
bamAllNumtSSorted.sql 18-Aug-2013 03:44 1.3K
bamAllNumtSSorted.txt.gz 18-Aug-2013 03:44 85
bigFiles.sql 09-Jul-2017 07:39 1.4K
bigFiles.txt.gz 09-Jul-2017 07:39 109
chainCanFam2.sql 02-Nov-2011 16:10 1.6K
chainCanFam2.txt.gz 02-Nov-2011 16:10 71M
chainCanFam2Link.sql 02-Nov-2011 12:13 1.5K
chainCanFam2Link.txt.gz 02-Nov-2011 12:18 650M
chainHg19.sql 02-Nov-2011 11:01 1.6K
chainHg19.txt.gz 02-Nov-2011 11:02 180M
chainHg19Link.sql 02-Nov-2011 15:21 1.5K
chainHg19Link.txt.gz 02-Nov-2011 15:26 835M
chainMm9.sql 02-Nov-2011 11:05 1.6K
chainMm9.txt.gz 02-Nov-2011 11:06 64M
chainMm9Link.sql 02-Nov-2011 15:56 1.5K
chainMm9Link.txt.gz 02-Nov-2011 15:59 491M
chainMonDom5.sql 02-Nov-2011 15:39 1.6K
chainMonDom5.txt.gz 02-Nov-2011 15:40 210M
chainMonDom5Link.sql 02-Nov-2011 11:46 1.5K
chainMonDom5Link.txt.gz 02-Nov-2011 11:50 656M
chainOrnAna1.sql 02-Nov-2011 11:07 1.6K
chainOrnAna1.txt.gz 02-Nov-2011 11:07 41M
chainOrnAna1Link.sql 02-Nov-2011 15:10 1.5K
chainOrnAna1Link.txt.gz 02-Nov-2011 15:11 234M
chainRn4.sql 02-Nov-2011 15:38 1.6K
chainRn4.txt.gz 02-Nov-2011 15:39 55M
chainRn4Link.sql 02-Nov-2011 15:43 1.5K
chainRn4Link.txt.gz 02-Nov-2011 15:46 455M
chainSusScr2.sql 02-Nov-2011 11:08 1.6K
chainSusScr2.txt.gz 02-Nov-2011 11:24 1.4G
chainSusScr2Link.sql 02-Nov-2011 12:36 1.5K
chainSusScr2Link.txt.gz 02-Nov-2011 13:33 6.9G
chromInfo.sql 02-Nov-2011 16:11 1.3K
chromInfo.txt.gz 02-Nov-2011 16:11 16K
cpgIslandExt.sql 02-Nov-2011 15:09 1.6K
cpgIslandExt.txt.gz 02-Nov-2011 15:09 811K
cpgIslandExtUnmasked.sql 01-Jun-2014 08:38 1.7K
cpgIslandExtUnmasked.txt.gz 01-Jun-2014 08:38 924K
ctgPos2.sql 02-Nov-2011 15:38 1.5K
ctgPos2.txt.gz 02-Nov-2011 15:38 47K
cytoBandIdeo.sql 11-Aug-2013 03:45 1.5K
cytoBandIdeo.txt.gz 11-Aug-2013 03:45 16K
ensGene.sql 20-Nov-2016 05:42 1.9K
ensGene.txt.gz 20-Nov-2016 05:42 2.3M
ensGtp.sql 20-Nov-2016 05:38 1.4K
ensGtp.txt.gz 20-Nov-2016 05:38 311K
ensPep.sql 20-Nov-2016 05:38 1.3K
ensPep.txt.gz 20-Nov-2016 05:38 6.7M
ensemblSource.sql 20-Nov-2016 05:42 1.4K
ensemblSource.txt.gz 20-Nov-2016 05:42 86K
ensemblToGeneName.sql 20-Nov-2016 05:42 1.4K
ensemblToGeneName.txt.gz 20-Nov-2016 05:42 154K
estOrientInfo.sql 19-Jun-2016 05:20 1.8K
estOrientInfo.txt.gz 19-Jun-2016 05:20 19M
gap.sql 02-Nov-2011 15:21 1.5K
gap.txt.gz 02-Nov-2011 15:21 1.0M
gbLoaded.sql 09-Jul-2017 07:39 1.6K
gbLoaded.txt.gz 09-Jul-2017 07:39 79K
gc5BaseBw.sql 02-Nov-2011 12:13 1.2K
gc5BaseBw.txt.gz 02-Nov-2011 12:13 63
gold.sql 02-Nov-2011 15:52 1.6K
gold.txt.gz 02-Nov-2011 15:52 1.3M
grp.sql 02-Mar-2014 03:37 1.3K
grp.txt.gz 02-Mar-2014 03:37 208
hgFindSpec.sql 09-Jul-2017 07:38 1.7K
hgFindSpec.txt.gz 09-Jul-2017 07:38 759
history.sql 02-Nov-2011 15:21 1.5K
history.txt.gz 02-Nov-2011 15:21 608
intronEst.sql 19-Jun-2016 05:20 2.1K
intronEst.txt.gz 19-Jun-2016 05:21 37M
microsat.sql 23-Aug-2015 10:22 1.5K
microsat.txt.gz 23-Aug-2015 10:22 275K
mrnaOrientInfo.sql 09-Jul-2017 07:39 1.8K
mrnaOrientInfo.txt.gz 09-Jul-2017 07:39 584K
nestedRepeats.sql 02-Nov-2011 12:36 1.9K
nestedRepeats.txt.gz 02-Nov-2011 12:36 15M
netCanFam2.sql 02-Nov-2011 12:11 2.0K
netCanFam2.txt.gz 02-Nov-2011 12:12 71M
netHg19.sql 02-Nov-2011 15:09 2.0K
netHg19.txt.gz 02-Nov-2011 15:09 66M
netMm9.sql 02-Nov-2011 15:17 2.0K
netMm9.txt.gz 02-Nov-2011 15:18 54M
netMonDom5.sql 02-Nov-2011 15:19 2.0K
netMonDom5.txt.gz 02-Nov-2011 15:19 17M
netOrnAna1.sql 02-Nov-2011 16:08 2.0K
netOrnAna1.txt.gz 02-Nov-2011 16:08 17M
netRn4.sql 02-Nov-2011 16:07 2.0K
netRn4.txt.gz 02-Nov-2011 16:08 52M
netSusScr2.sql 02-Nov-2011 16:08 2.0K
netSusScr2.txt.gz 02-Nov-2011 16:09 65M
numtS.sql 18-Aug-2013 03:44 1.7K
numtS.txt.gz 18-Aug-2013 03:44 8.8K
numtSAssembled.sql 18-Aug-2013 03:44 1.8K
numtSAssembled.txt.gz 18-Aug-2013 03:44 2.7K
numtSMitochondrion.sql 18-Aug-2013 03:44 1.6K
numtSMitochondrion.txt.gz 18-Aug-2013 03:44 2.4K
refFlat.sql 09-Jul-2017 07:38 1.7K
refFlat.txt.gz 09-Jul-2017 07:38 1.4M
refGene.sql 09-Jul-2017 07:38 1.9K
refGene.txt.gz 09-Jul-2017 07:38 1.5M
refSeqAli.sql 09-Jul-2017 07:38 2.1K
refSeqAli.txt.gz 09-Jul-2017 07:38 1.5M
rmsk.sql 02-Nov-2011 15:15 1.8K
rmsk.txt.gz 02-Nov-2011 15:15 135M
simpleRepeat.sql 02-Nov-2011 15:09 1.9K
simpleRepeat.txt.gz 02-Nov-2011 15:09 12M
tRNAs.sql 15-Apr-2012 15:40 1.7K
tRNAs.txt.gz 15-Apr-2012 15:40 107K
tableDescriptions.sql 09-Jul-2017 07:39 1.4K
tableDescriptions.txt.gz 09-Jul-2017 07:39 5.0K
tableList.sql 09-Jul-2017 07:35 1.5K
tableList.txt.gz 09-Jul-2017 07:35 3.6K
trackDb.sql 09-Jul-2017 07:35 2.0K
trackDb.txt.gz 09-Jul-2017 07:35 32K
ucscToEnsembl.sql 02-Nov-2011 12:36 1.3K
ucscToEnsembl.txt.gz 02-Nov-2011 12:36 19K
xenoMrna.sql 09-Jul-2017 07:35 2.1K
xenoMrna.txt.gz 09-Jul-2017 07:36 317M
xenoRefFlat.sql 09-Jul-2017 07:38 1.7K
xenoRefFlat.txt.gz 09-Jul-2017 07:38 26M
xenoRefGene.sql 09-Jul-2017 07:39 1.9K
xenoRefGene.txt.gz 09-Jul-2017 07:39 28M
xenoRefSeqAli.sql 09-Jul-2017 07:38 2.1K
xenoRefSeqAli.txt.gz 09-Jul-2017 07:38 28M