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.

---------------------------------------------------------------
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 - all_mrna.sql 2019-03-17 09:47 2.1K all_mrna.txt.gz 2019-03-17 09:47 20K augustusGene.sql 2015-07-26 14:02 1.9K augustusGene.txt.gz 2015-07-26 14:02 1.8M bigFiles.sql 2021-05-16 03:09 1.4K bigFiles.txt.gz 2021-05-16 03:09 68 chainMm10.sql 2012-05-11 12:52 1.6K chainMm10.txt.gz 2012-05-11 12:53 55M chainMm10Link.sql 2012-05-11 13:50 1.5K chainMm10Link.txt.gz 2012-05-11 13:54 520M chromAlias.sql 2018-08-05 06:53 1.4K chromAlias.txt.gz 2018-08-05 06:53 178K chromInfo.sql 2012-05-11 14:45 1.3K chromInfo.txt.gz 2012-05-11 14:45 134K cpgIslandExt.sql 2012-05-11 14:39 1.6K cpgIslandExt.txt.gz 2012-05-11 14:39 652K cpgIslandExtUnmasked.sql 2014-06-01 13:50 1.7K cpgIslandExtUnmasked.txt.gz 2014-06-01 13:50 698K ensGene.sql 2020-08-31 15:35 1.9K ensGene.txt.gz 2020-08-31 15:35 2.5M ensGtp.sql 2020-08-31 15:35 1.4K ensGtp.txt.gz 2020-08-31 15:35 392K ensPep.sql 2020-08-31 15:57 1.3K ensPep.txt.gz 2020-08-31 15:57 6.1M ensemblSource.sql 2020-08-31 15:57 1.4K ensemblSource.txt.gz 2020-08-31 15:57 105K ensemblToGeneName.sql 2020-08-31 15:35 1.4K ensemblToGeneName.txt.gz 2020-08-31 15:35 131K gap.sql 2012-05-11 13:07 1.5K gap.txt.gz 2012-05-11 13:07 3.0M gbLoaded.sql 2020-08-22 02:43 1.6K gbLoaded.txt.gz 2020-08-22 02:43 41K gc5BaseBw.sql 2012-05-11 13:50 1.2K gc5BaseBw.txt.gz 2012-05-11 13:50 63 genscan.sql 2012-05-11 14:38 1.6K genscan.txt.gz 2012-05-11 14:38 2.4M genscanPep.sql 2012-05-11 15:11 1.3K genscanPep.txt.gz 2012-05-11 15:11 7.9M genscanSubopt.sql 2012-05-11 14:39 1.5K genscanSubopt.txt.gz 2012-05-11 14:39 5.9M gold.sql 2012-05-11 15:10 1.6K gold.txt.gz 2012-05-11 15:10 3.9M grp.sql 2014-03-02 04:14 1.3K grp.txt.gz 2014-03-02 04:14 208 hgFindSpec.sql 2020-10-25 08:05 1.7K hgFindSpec.txt.gz 2020-10-25 08:05 650 history.sql 2012-05-11 14:38 1.5K history.txt.gz 2012-05-11 14:38 410 microsat.sql 2015-08-23 17:28 1.5K microsat.txt.gz 2015-08-23 17:28 371K mrnaOrientInfo.sql 2019-03-17 09:44 1.8K mrnaOrientInfo.txt.gz 2019-03-17 09:44 3.2K nestedRepeats.sql 2012-05-11 15:11 1.9K nestedRepeats.txt.gz 2012-05-11 15:11 10M netMm10.sql 2012-05-11 15:06 2.0K netMm10.txt.gz 2012-05-11 15:08 64M rmsk.sql 2012-05-11 12:57 1.8K rmsk.txt.gz 2012-05-11 12:59 106M simpleRepeat.sql 2012-05-11 14:38 1.9K simpleRepeat.txt.gz 2012-05-11 14:38 17M tableDescriptions.sql 2019-07-21 03:41 1.4K tableDescriptions.txt.gz 2019-07-21 03:41 5.2K tableList.sql 2021-05-16 03:09 1.6K tableList.txt.gz 2021-05-16 03:09 2.2K trackDb.sql 2020-10-25 08:05 2.0K trackDb.txt.gz 2020-10-25 08:05 21K windowmaskerSdust.sql 2012-05-11 15:11 1.4K windowmaskerSdust.txt.gz 2012-05-11 15:13 129M xenoMrna.sql 2020-08-22 02:23 2.1K xenoMrna.txt.gz 2020-08-22 02:23 431M xenoRefFlat.sql 2020-08-22 02:30 1.7K xenoRefFlat.txt.gz 2020-08-22 02:30 39M xenoRefGene.sql 2020-08-22 02:30 1.9K xenoRefGene.txt.gz 2020-08-22 02:30 43M xenoRefSeqAli.sql 2020-08-22 02:30 2.1K xenoRefSeqAli.txt.gz 2020-08-22 02:30 42M