This directory contains a dump of the UCSC genome annotation database for
the Mar. 2007 assembly of the tetraodon genome
(tetNig2, Genoscope Tetraodon v8.0 (NCBI project 12350, CAAE01000000)).
The annotations were generated by UCSC and collaborators worldwide.

This assembly was produced by Genoscope - Centre National de Séquençage
and the Broad Institute.

For more information on the tetraodon genome, see the project website:
http://www.genoscope.cns.fr/spip/
http://www.genoscope.cns.fr/spip/Tetraodon-nigroviridis-a-fish-with.html
http://www.broadinstitute.org/annotation/tetraodon/background.html

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=tetNig2
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/tetNig2/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/tetNig2/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/tetNig2/database/gc5BaseBw.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/tetNig2/database/*'
With wget, a single file: 
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/tetNig2/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 tetNig2 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql tetNig2 --local-infile=1 
        -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'


The Tetraodon sequence has been freely provided by Genoscope before
publication for use in the UCSC Genome Browser with the following
understanding:

1. The data may be freely downloaded, used in analyses, and repackaged
   in databases.
2. Users are free to use the data in scientific papers analyzing particular
   genes and regions, provided that the Genoscope is properly acknowledged.
3. Genoscope reserves the right to publish the initial large-scale analyses
   of the dataset, including large-scale identification of regions of
   evolutionary conservation and large-scale genomic assembly. Large-scale
   refers to regions with size on the order of a Tetraodon chromosome (that
   is, 5 Mb or more).
4. Any redistribution of the data should carry this notice.
      Name                        Last modified      Size  Description
Parent Directory - gold.sql 2010-03-10 13:26 1.7K gold.txt.gz 2010-03-10 13:26 297K netHg19.sql 2010-03-10 13:26 2.3K netHg19.txt.gz 2010-03-10 13:26 5.0M chainHg19.sql 2010-03-10 13:26 1.8K chainHg19.txt.gz 2010-03-10 13:26 6.9M gap.sql 2010-03-10 13:26 1.6K gap.txt.gz 2010-03-10 13:26 437K gc5Base.sql 2010-03-10 13:26 1.9K gc5Base.txt.gz 2010-03-10 13:26 1.4M chainOryLat2.sql 2010-03-10 13:26 1.6K chainOryLat2.txt.gz 2010-03-10 13:26 21M history.sql 2010-03-10 13:26 1.6K history.txt.gz 2010-03-10 13:26 1.3K windowmaskerSdust.sql 2010-03-10 13:26 1.5K windowmaskerSdust.txt.gz 2010-03-10 13:26 15M blastHg18KG.sql 2010-03-10 13:27 2.3K blastHg18KG.txt.gz 2010-03-10 13:27 2.8M nestedRepeats.sql 2010-03-10 13:27 2.0K nestedRepeats.txt.gz 2010-03-10 13:27 52K cpgIslandExt.sql 2010-03-10 13:27 1.6K cpgIslandExt.txt.gz 2010-03-10 13:27 774K simpleRepeat.sql 2010-03-10 13:28 2.0K simpleRepeat.txt.gz 2010-03-10 13:28 3.5M netOryLat2.sql 2010-03-10 13:28 2.0K netOryLat2.txt.gz 2010-03-10 13:29 11M chainHg19Link.sql 2010-03-10 13:30 1.5K chainHg19Link.txt.gz 2010-03-10 13:30 42M netGasAcu1.sql 2010-03-10 13:30 2.0K netGasAcu1.txt.gz 2010-03-10 13:31 9.8M gaze.sql 2010-03-10 13:31 1.6K gaze.txt.gz 2010-03-10 13:31 1.8M chainGasAcu1.sql 2010-03-10 13:33 1.6K chainGasAcu1.txt.gz 2010-03-10 13:33 16M chainGasAcu1Link.sql 2010-03-10 13:34 1.5K chainGasAcu1Link.txt.gz 2010-03-10 13:34 83M gazePep.sql 2010-03-10 13:34 1.3K gazePep.txt.gz 2010-03-10 13:34 6.1M chainOryLat2Link.sql 2010-03-10 13:34 1.5K chainOryLat2Link.txt.gz 2010-03-10 13:35 128M chromInfo.sql 2010-03-10 13:35 1.3K chromInfo.txt.gz 2010-03-10 13:35 274 netDanRer7.sql 2011-03-24 09:25 2.0K netDanRer7.txt.gz 2011-03-24 09:25 7.6M chainDanRer7Link.sql 2011-03-24 09:25 1.5K chainDanRer7Link.txt.gz 2011-03-24 09:26 88M chainDanRer7.sql 2011-03-24 09:27 1.6K chainDanRer7.txt.gz 2011-03-24 09:28 24M tRNAs.sql 2012-04-16 05:37 1.7K tRNAs.txt.gz 2012-04-16 05:37 13K chainFr3.sql 2012-05-28 15:09 1.6K chainFr3.txt.gz 2012-05-28 15:09 12M netFr3.sql 2012-05-28 15:09 2.0K netFr3.txt.gz 2012-05-28 15:09 12M chainFr3Link.sql 2012-05-28 15:09 1.5K chainFr3Link.txt.gz 2012-05-28 15:10 106M cytoBandIdeo.sql 2013-04-28 22:33 1.5K cytoBandIdeo.txt.gz 2013-04-28 22:33 473 chainMm10.sql 2013-10-27 22:09 1.7K chainMm10.txt.gz 2013-10-27 22:09 3.9M chainMm10Link.sql 2013-10-27 22:09 1.5K chainMm10Link.txt.gz 2013-10-27 22:09 28M netMm10.sql 2013-10-27 22:09 2.1K netMm10.txt.gz 2013-10-27 22:09 4.7M genscan.sql 2013-12-10 06:25 1.7K genscan.txt.gz 2013-12-10 06:25 1.2M grp.sql 2014-03-02 04:18 1.4K grp.txt.gz 2014-03-02 04:18 199 cpgIslandExtUnmasked.sql 2014-06-01 20:09 1.7K cpgIslandExtUnmasked.txt.gz 2014-06-01 20:09 1.0M augustusGene.sql 2015-07-26 17:28 1.9K augustusGene.txt.gz 2015-07-26 17:28 2.5M microsat.sql 2015-08-24 02:42 1.5K microsat.txt.gz 2015-08-24 02:42 223K chr2_random_mrna.sql 2016-07-03 09:13 2.1K chr2_random_mrna.txt.gz 2016-07-03 09:13 19K chr5_mrna.sql 2016-07-03 09:13 2.1K chr5_mrna.txt.gz 2016-07-03 09:13 236K chr10_mrna.sql 2016-07-03 09:13 2.1K chr10_mrna.txt.gz 2016-07-03 09:13 123K chr21_random_mrna.sql 2016-07-03 09:13 2.1K chr21_random_mrna.txt.gz 2016-07-03 09:13 34K chr1_mrna.sql 2016-07-03 09:13 2.1K chr1_mrna.txt.gz 2016-07-03 09:13 281K chr12_mrna.sql 2016-07-03 09:13 2.1K chr12_mrna.txt.gz 2016-07-03 09:13 115K chr14_mrna.sql 2016-07-03 09:13 2.1K chr14_mrna.txt.gz 2016-07-03 09:13 140K chr17_mrna.sql 2016-07-03 09:13 2.1K chr17_mrna.txt.gz 2016-07-03 09:13 97K chrM_mrna.sql 2016-07-03 09:13 2.1K chrM_mrna.txt.gz 2016-07-03 09:13 4.3K chr13_mrna.sql 2016-07-03 09:13 2.1K chr13_mrna.txt.gz 2016-07-03 09:13 242K chr20_mrna.sql 2016-07-03 09:13 2.1K chr20_mrna.txt.gz 2016-07-03 09:13 24K chr6_mrna.sql 2016-07-03 09:14 2.1K chr6_mrna.txt.gz 2016-07-03 09:14 68K chr8_mrna.sql 2016-07-03 09:14 2.1K chr8_mrna.txt.gz 2016-07-03 09:14 125K chr11_mrna.sql 2016-07-03 09:14 2.1K chr11_mrna.txt.gz 2016-07-03 09:14 130K chr15_mrna.sql 2016-07-03 09:14 2.1K chr18_mrna.sql 2016-07-03 09:14 2.1K chr18_mrna.txt.gz 2016-07-03 09:14 165K chr15_mrna.txt.gz 2016-07-03 09:14 103K chr2_mrna.sql 2016-07-03 09:14 2.1K chr2_mrna.txt.gz 2016-07-03 09:14 219K chr19_mrna.sql 2016-07-03 09:14 2.1K chr19_mrna.txt.gz 2016-07-03 09:14 48K chr1_random_mrna.sql 2016-07-03 09:15 2.1K chr1_random_mrna.txt.gz 2016-07-03 09:15 8.7K chr3_mrna.sql 2016-07-03 09:15 2.1K chr3_mrna.txt.gz 2016-07-03 09:15 335K chr7_mrna.sql 2016-07-03 09:15 2.1K chr7_mrna.txt.gz 2016-07-03 09:15 144K chr15_random_mrna.sql 2016-07-03 09:15 2.1K chr15_random_mrna.txt.gz 2016-07-03 09:15 31K chr21_mrna.sql 2016-07-03 09:15 2.1K chr21_mrna.txt.gz 2016-07-03 09:15 77K chrUn_random_mrna.sql 2016-07-03 09:15 2.1K chrUn_random_mrna.txt.gz 2016-07-03 09:15 1.1M chr9_mrna.sql 2016-12-04 09:06 2.1K chr9_mrna.txt.gz 2016-12-04 09:06 127K chr16_mrna.sql 2016-12-04 09:06 2.1K chr16_mrna.txt.gz 2016-12-04 09:06 156K chromAlias.sql 2018-08-05 09:35 1.4K chromAlias.txt.gz 2018-08-05 09:35 178 chainGalGal6.sql 2019-01-20 20:24 1.7K chainGalGal6.txt.gz 2019-01-20 20:24 4.9M chainGalGal6Link.sql 2019-01-20 20:24 1.5K chainGalGal6Link.txt.gz 2019-01-20 20:24 34M netGalGal6.sql 2019-01-20 20:24 2.1K netGalGal6.txt.gz 2019-01-20 20:24 5.1M tableDescriptions.sql 2019-07-21 03:43 1.4K tableDescriptions.txt.gz 2019-07-21 03:43 5.8K all_mrna.sql 2019-10-20 12:03 2.1K all_mrna.txt.gz 2019-10-20 12:03 4.2M chr4_mrna.sql 2019-10-20 12:03 2.1K chr4_mrna.txt.gz 2019-10-20 12:03 127K mrnaOrientInfo.sql 2019-10-20 12:05 1.8K mrnaOrientInfo.txt.gz 2019-10-20 12:05 876K xenoMrna.sql 2020-08-20 14:18 2.1K xenoMrna.txt.gz 2020-08-20 14:18 196M gbLoaded.sql 2020-08-20 14:43 1.6K xenoRefFlat.sql 2020-08-20 14:43 1.7K xenoRefGene.sql 2020-08-20 14:43 1.9K xenoRefSeqAli.sql 2020-08-20 14:43 2.1K xenoRefGene.txt.gz 2020-08-20 14:43 22M xenoRefFlat.txt.gz 2020-08-20 14:43 20M xenoRefSeqAli.txt.gz 2020-08-20 14:43 18M gbLoaded.txt.gz 2020-08-20 14:43 15K ensGene.sql 2021-05-25 14:50 1.9K ensGene.txt.gz 2021-05-25 14:50 2.1M ensGtp.sql 2021-05-25 14:50 1.4K ensGtp.txt.gz 2021-05-25 14:50 217K ensemblToGeneName.sql 2021-05-25 14:50 1.4K ensemblToGeneName.txt.gz 2021-05-25 14:50 130K ensemblSource.sql 2021-05-25 14:53 1.4K ensemblSource.txt.gz 2021-05-25 14:53 64K ensPep.sql 2021-05-25 14:53 1.3K ensPep.txt.gz 2021-05-25 14:53 6.9M trackDb.sql 2021-06-10 16:56 2.1K trackDb.txt.gz 2021-06-10 16:56 39K hgFindSpec.sql 2021-06-10 16:56 1.8K hgFindSpec.txt.gz 2021-06-10 16:56 867 tableList.sql 2021-06-13 03:05 1.6K tableList.txt.gz 2021-06-13 03:05 5.0K bigFiles.sql 2021-06-13 03:05 1.4K bigFiles.txt.gz 2021-06-13 03:05 33