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.
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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/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 -
chainMm10Link.txt.gz 2013-10-27 17:12 315M
xenoMrna.txt.gz 2016-02-21 19:11 253M
windowmaskerSdust.txt.gz 2012-01-19 11:21 156M
rmsk.txt.gz 2012-01-19 11:22 142M
chainMm10.txt.gz 2013-10-27 17:12 84M
xenoRefSeqAli.txt.gz 2020-08-19 14:23 30M
xenoRefGene.txt.gz 2020-08-19 14:23 29M
xenoRefFlat.txt.gz 2020-08-19 14:23 26M
simpleRepeat.txt.gz 2012-01-19 11:27 18M
gold.txt.gz 2012-01-19 11:24 18M
nestedRepeats.txt.gz 2012-01-19 11:27 12M
netMm10.txt.gz 2013-10-27 17:12 12M
all_est.txt.gz 2017-05-14 07:20 12M
gap.txt.gz 2012-01-19 11:16 9.3M
intronEst.txt.gz 2017-05-14 07:20 5.4M
estOrientInfo.txt.gz 2017-05-14 07:20 3.4M
chromAlias.txt.gz 2016-09-15 17:59 2.4M
genscan.txt.gz 2013-12-10 01:59 2.2M
ucscToINSDC.txt.gz 2013-09-15 15:55 2.1M
augustusGene.txt.gz 2015-07-26 16:14 1.6M
cytoBandIdeo.txt.gz 2013-04-28 18:15 1.4M
chromInfo.txt.gz 2012-01-19 11:24 1.4M
microsat.txt.gz 2015-08-23 20:50 700K
trackDb.txt.gz 2023-03-28 13:50 32K
gbLoaded.txt.gz 2020-08-19 14:23 30K
all_mrna.txt.gz 2017-11-05 08:25 22K
mrnaOrientInfo.txt.gz 2017-11-05 08:25 5.8K
tableDescriptions.txt.gz 2024-11-23 02:03 4.9K
xenoRefSeqAli.sql 2020-08-19 14:23 2.1K
intronEst.sql 2017-05-14 07:20 2.1K
xenoMrna.sql 2016-02-21 19:11 2.1K
all_mrna.sql 2017-11-05 08:25 2.1K
tableList.txt.gz 2024-11-24 03:31 2.1K
all_est.sql 2017-05-14 07:20 2.1K
netMm10.sql 2013-10-27 17:12 2.1K
trackDb.sql 2023-03-28 13:50 2.1K
xenoRefGene.sql 2020-08-19 14:23 2.0K
augustusGene.sql 2015-07-26 16:14 1.9K
nestedRepeats.sql 2012-01-19 11:27 1.9K
simpleRepeat.sql 2012-01-19 11:27 1.9K
rmsk.sql 2012-01-19 11:22 1.8K
mrnaOrientInfo.sql 2017-11-05 08:25 1.8K
estOrientInfo.sql 2017-05-14 07:20 1.8K
hgFindSpec.sql 2023-03-28 13:50 1.8K
xenoRefFlat.sql 2020-08-19 14:23 1.7K
chainMm10.sql 2013-10-27 17:12 1.7K
genscan.sql 2013-12-10 01:59 1.7K
gbLoaded.sql 2020-08-19 14:23 1.6K
gold.sql 2012-01-19 11:24 1.6K
tableList.sql 2024-11-24 03:31 1.6K
chainMm10Link.sql 2013-10-27 17:12 1.5K
gap.sql 2012-01-19 11:16 1.5K
cytoBandIdeo.sql 2013-04-28 18:15 1.5K
history.sql 2012-01-19 11:25 1.5K
microsat.sql 2015-08-23 20:50 1.5K
tableDescriptions.sql 2024-11-23 02:03 1.5K
chromAlias.sql 2016-09-15 17:59 1.4K
windowmaskerSdust.sql 2012-01-19 11:20 1.4K
ucscToINSDC.sql 2013-09-15 15:55 1.4K
bigFiles.sql 2024-11-24 03:31 1.4K
grp.sql 2014-03-02 04:14 1.3K
chromInfo.sql 2012-01-19 11:24 1.3K
gc5BaseBw.sql 2012-01-19 11:20 1.2K
hgFindSpec.txt.gz 2023-03-28 13:50 619
history.txt.gz 2012-01-19 11:25 270
grp.txt.gz 2014-03-02 04:14 208
bigFiles.txt.gz 2024-11-24 03:31 68
gc5BaseBw.txt.gz 2012-01-19 11:20 63