This directory contains a dump of the UCSC genome annotation database for
the Jul. 2011 (HetGla_1.0/hetGla1) assembly of the naked mole-rat genome (hetGla1, HetGla_1.0 (NCBI project 68323, accession GCA_000230455.1)).
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 naked mole-rat genome, see the project website:
http://www.ncbi.nlm.nih.gov/bioproject/68323
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=hetGla1
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/hetGla1/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/hetGla1/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/hetGla1/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/hetGla1/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/hetGla1/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 hetGla1 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql hetGla1 --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 -
chainMm10.sql 2012-05-11 12:52 1.6K
chainMm10.txt.gz 2012-05-11 12:53 55M
rmsk.sql 2012-05-11 12:57 1.8K
rmsk.txt.gz 2012-05-11 12:59 106M
gap.sql 2012-05-11 13:07 1.5K
gap.txt.gz 2012-05-11 13:07 3.0M
gc5BaseBw.sql 2012-05-11 13:50 1.2K
gc5BaseBw.txt.gz 2012-05-11 13:50 63
chainMm10Link.sql 2012-05-11 13:50 1.5K
chainMm10Link.txt.gz 2012-05-11 13:54 520M
genscan.sql 2012-05-11 14:38 1.6K
genscan.txt.gz 2012-05-11 14:38 2.4M
history.sql 2012-05-11 14:38 1.5K
history.txt.gz 2012-05-11 14:38 410
simpleRepeat.sql 2012-05-11 14:38 1.9K
simpleRepeat.txt.gz 2012-05-11 14:38 17M
genscanSubopt.sql 2012-05-11 14:39 1.5K
genscanSubopt.txt.gz 2012-05-11 14:39 5.9M
cpgIslandExt.sql 2012-05-11 14:39 1.6K
cpgIslandExt.txt.gz 2012-05-11 14:39 652K
chromInfo.sql 2012-05-11 14:45 1.3K
chromInfo.txt.gz 2012-05-11 14:45 134K
netMm10.sql 2012-05-11 15:06 2.0K
netMm10.txt.gz 2012-05-11 15:08 64M
gold.sql 2012-05-11 15:10 1.6K
gold.txt.gz 2012-05-11 15:10 3.9M
genscanPep.sql 2012-05-11 15:11 1.3K
genscanPep.txt.gz 2012-05-11 15:11 7.9M
nestedRepeats.sql 2012-05-11 15:11 1.9K
nestedRepeats.txt.gz 2012-05-11 15:11 10M
windowmaskerSdust.sql 2012-05-11 15:11 1.4K
windowmaskerSdust.txt.gz 2012-05-11 15:13 129M
grp.sql 2014-03-02 04:14 1.3K
grp.txt.gz 2014-03-02 04:14 208
cpgIslandExtUnmasked.sql 2014-06-01 13:50 1.7K
cpgIslandExtUnmasked.txt.gz 2014-06-01 13:50 698K
augustusGene.sql 2015-07-26 14:02 1.9K
augustusGene.txt.gz 2015-07-26 14:02 1.8M
microsat.sql 2015-08-23 17:28 1.5K
microsat.txt.gz 2015-08-23 17:28 371K
chromAlias.sql 2018-08-05 06:53 1.4K
chromAlias.txt.gz 2018-08-05 06:53 178K
mrnaOrientInfo.sql 2019-03-17 09:44 1.8K
mrnaOrientInfo.txt.gz 2019-03-17 09:44 3.2K
all_mrna.sql 2019-03-17 09:47 2.1K
all_mrna.txt.gz 2019-03-17 09:47 20K
xenoMrna.sql 2020-08-22 02:23 2.1K
xenoMrna.txt.gz 2020-08-22 02:23 431M
xenoRefGene.sql 2020-08-22 02:30 2.0K
xenoRefGene.txt.gz 2020-08-22 02:30 43M
xenoRefFlat.sql 2020-08-22 02:30 1.7K
xenoRefFlat.txt.gz 2020-08-22 02:30 39M
xenoRefSeqAli.sql 2020-08-22 02:30 2.1K
xenoRefSeqAli.txt.gz 2020-08-22 02:30 42M
gbLoaded.sql 2020-08-22 02:43 1.6K
gbLoaded.txt.gz 2020-08-22 02:43 41K
ensGene.sql 2021-05-25 14:33 1.9K
ensGene.txt.gz 2021-05-25 14:33 2.5M
ensGtp.sql 2021-05-25 14:33 1.4K
ensGtp.txt.gz 2021-05-25 14:33 383K
ensemblToGeneName.sql 2021-05-25 14:33 1.4K
ensemblToGeneName.txt.gz 2021-05-25 14:33 11K
ensemblSource.sql 2021-05-25 14:35 1.4K
ensemblSource.txt.gz 2021-05-25 14:35 105K
ensPep.sql 2021-05-25 14:35 1.3K
ensPep.txt.gz 2021-05-25 14:35 6.1M
trackDb.sql 2023-03-28 13:50 2.1K
trackDb.txt.gz 2023-03-28 13:50 20K
hgFindSpec.sql 2023-03-28 13:50 1.8K
hgFindSpec.txt.gz 2023-03-28 13:50 701
tableDescriptions.sql 2024-11-16 02:03 1.4K
tableDescriptions.txt.gz 2024-11-16 02:03 5.2K
tableList.sql 2024-11-17 03:36 1.6K
tableList.txt.gz 2024-11-17 03:36 2.2K
bigFiles.sql 2024-11-17 03:36 1.4K
bigFiles.txt.gz 2024-11-17 03:36 68