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