This directory contains a dump of the UCSC genome annotation database for
the Sep. 2009 (TWGS Meug_1.1/macEug2) assembly of the wallaby genome (macEug2, TWGS (NCBI Project ID: 12586, Accession: GCA_000004035.1)).
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 wallaby genome, see the project website:
http://www.ncbi.nlm.nih.gov/bioproject/12587

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=macEug2
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/macEug2/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/macEug2/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/macEug2/database/gc5BaseBw.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/macEug2/database/*'
With wget, a single file: 
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/macEug2/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 macEug2 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql macEug2 --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 2017-05-14 07:20 2.1K all_est.txt.gz 2017-05-14 07:20 12M all_mrna.sql 2017-11-05 08:25 2.1K all_mrna.txt.gz 2017-11-05 08:25 22K augustusGene.sql 2015-07-26 16:14 1.9K augustusGene.txt.gz 2015-07-26 16:14 1.6M bigFiles.sql 2021-05-02 03:11 1.4K bigFiles.txt.gz 2021-05-02 03:11 68 chainMm10.sql 2013-10-27 17:12 1.7K chainMm10.txt.gz 2013-10-27 17:12 84M chainMm10Link.sql 2013-10-27 17:12 1.5K chainMm10Link.txt.gz 2013-10-27 17:12 315M chromAlias.sql 2016-09-15 17:59 1.4K chromAlias.txt.gz 2016-09-15 17:59 2.4M chromInfo.sql 2012-01-19 11:24 1.3K chromInfo.txt.gz 2012-01-19 11:24 1.4M cytoBandIdeo.sql 2013-04-28 18:15 1.5K cytoBandIdeo.txt.gz 2013-04-28 18:15 1.4M estOrientInfo.sql 2017-05-14 07:20 1.8K estOrientInfo.txt.gz 2017-05-14 07:20 3.4M gap.sql 2012-01-19 11:16 1.5K gap.txt.gz 2012-01-19 11:16 9.3M gbLoaded.sql 2020-08-19 14:23 1.6K gbLoaded.txt.gz 2020-08-19 14:23 30K gc5BaseBw.sql 2012-01-19 11:20 1.2K gc5BaseBw.txt.gz 2012-01-19 11:20 63 genscan.sql 2013-12-10 01:59 1.7K genscan.txt.gz 2013-12-10 01:59 2.2M gold.sql 2012-01-19 11:24 1.6K gold.txt.gz 2012-01-19 11:24 18M grp.sql 2014-03-02 04:14 1.3K grp.txt.gz 2014-03-02 04:14 208 hgFindSpec.sql 2020-12-06 08:08 1.7K hgFindSpec.txt.gz 2020-12-06 08:08 570 history.sql 2012-01-19 11:25 1.5K history.txt.gz 2012-01-19 11:25 270 intronEst.sql 2017-05-14 07:20 2.1K intronEst.txt.gz 2017-05-14 07:20 5.4M microsat.sql 2015-08-23 20:50 1.5K microsat.txt.gz 2015-08-23 20:50 700K mrnaOrientInfo.sql 2017-11-05 08:25 1.8K mrnaOrientInfo.txt.gz 2017-11-05 08:25 5.8K nestedRepeats.sql 2012-01-19 11:27 1.9K nestedRepeats.txt.gz 2012-01-19 11:27 12M netMm10.sql 2013-10-27 17:12 2.1K netMm10.txt.gz 2013-10-27 17:12 12M rmsk.sql 2012-01-19 11:22 1.8K rmsk.txt.gz 2012-01-19 11:22 142M simpleRepeat.sql 2012-01-19 11:27 1.9K simpleRepeat.txt.gz 2012-01-19 11:27 18M tableDescriptions.sql 2020-10-10 02:03 1.4K tableDescriptions.txt.gz 2020-10-10 02:03 4.8K tableList.sql 2021-05-02 03:11 1.6K tableList.txt.gz 2021-05-02 03:11 2.1K trackDb.sql 2020-12-04 03:06 2.0K trackDb.txt.gz 2020-12-04 03:06 31K ucscToINSDC.sql 2013-09-15 15:55 1.4K ucscToINSDC.txt.gz 2013-09-15 15:55 2.1M windowmaskerSdust.sql 2012-01-19 11:20 1.4K windowmaskerSdust.txt.gz 2012-01-19 11:21 156M xenoMrna.sql 2016-02-21 19:11 2.1K xenoMrna.txt.gz 2016-02-21 19:11 253M xenoRefFlat.sql 2020-08-19 14:23 1.7K xenoRefFlat.txt.gz 2020-08-19 14:23 26M xenoRefGene.sql 2020-08-19 14:23 1.9K xenoRefGene.txt.gz 2020-08-19 14:23 29M xenoRefSeqAli.sql 2020-08-19 14:23 2.1K xenoRefSeqAli.txt.gz 2020-08-19 14:23 30M