This directory contains a dump of the UCSC genome annotation database for
the Oct. 2011 (FUGU5/fr3) assembly of the fugu genome
(fr3, Fugu Genome Sequencing Consortium - FUGU5
(NCBI project 1434, GCA_000180615.2)).
The annotations were generated by UCSC and collaborators worldwide.
This assembly was produced by the Fugu Genome Sequencing Consortium,
as part of the International Fugu Genome Consortium, led by JGI and the
Singapore Institute of Molecular and Cell Biology (IMCB).
For more information on the fugu genome, see the project website:
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:
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/fr3/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/fr3/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
Or with wget, all files:
With wget, a single file:
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:
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 fr3 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql fr3 --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.
1. These data have been freely provided by the JGI for use in the
UCSC Genome Browser.
Apache/2.2.15 (CentOS) Server at hgdownload-test.sdsc.edu Port 80