This directory contains a dump of the UCSC genome annotation database for
the Nov. 2011 (ICGSC Gallus_gallus-4.0/galGal4) assembly of the chicken genome (galGal4, ICGSC Gallus_gallus-4.0 (GCA_000002315.2))
from the Chicken Genome Sequencing Consortium.
The annotations were generated by UCSC and collaborators worldwide.

For more information about this assembly, please note the NCBI resources:
    http://www.ncbi.nlm.nih.gov/genome/111
    http://www.ncbi.nlm.nih.gov/genome/assembly/317958
    http://www.ncbi.nlm.nih.gov/bioproject/13342

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=galGal4
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/galGal4/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/galGal4/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/galGal4/database/gc5BaseBw.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/galGal4/database/*'
With wget, a single file: 
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/galGal4/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 galGal4 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql galGal4 --local-infile=1 
        -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'

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The Chicken sequence is made freely available to the community by the
Genome Sequencing Center, Washington University School of Medicine, 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 these data
   if the providers of these data are properly cited:
   International Chicken Genome Sequencing Consortium.  
   Sequence and comparative analysis of the chicken genome provide unique
   perspectives on vertebrate evolution.
   Nature. 2004 Dec 9;432(7018):695-716.  PMID: 15592404
   See http://genome.ucsc.edu/goldenPath/credits.html for credit information.

3. Any redistribution of the data should carry this notice.

All the files and tables in this directory are freely usable for any purpose.

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      Name                        Last modified      Size  Description
Parent Directory - history.sql 2012-06-11 06:20 1.5K history.txt.gz 2012-06-11 06:20 392 genscan.sql 2012-06-11 06:20 1.6K genscan.txt.gz 2012-06-11 06:20 1.4M gold.sql 2012-06-11 06:20 1.6K gold.txt.gz 2012-06-11 06:20 213K genscanSubopt.sql 2012-06-11 06:20 1.5K genscanSubopt.txt.gz 2012-06-11 06:21 2.8M chromInfo.sql 2012-06-11 06:21 1.3K chromInfo.txt.gz 2012-06-11 06:21 78K simpleRepeat.sql 2012-06-11 06:21 1.9K simpleRepeat.txt.gz 2012-06-11 06:21 4.9M cpgIslandExt.sql 2012-06-11 06:23 1.6K cpgIslandExt.txt.gz 2012-06-11 06:23 472K windowmaskerSdust.sql 2012-06-11 06:58 1.4K windowmaskerSdust.txt.gz 2012-06-11 06:59 54M netMm10.sql 2012-06-11 07:08 2.0K netMm10.txt.gz 2012-06-11 07:09 7.7M gap.sql 2012-06-11 07:11 1.5K gap.txt.gz 2012-06-11 07:11 181K nestedRepeats.sql 2012-06-11 07:25 1.9K nestedRepeats.txt.gz 2012-06-11 07:25 671K chainMm10.sql 2012-06-11 07:27 1.6K chainMm10.txt.gz 2012-06-11 07:27 7.2M rmsk.sql 2012-06-11 07:45 1.8K rmsk.txt.gz 2012-06-11 07:45 14M chainMm10Link.sql 2012-06-11 07:47 1.5K chainMm10Link.txt.gz 2012-06-11 07:48 53M gc5BaseBw.sql 2012-06-11 07:51 1.2K gc5BaseBw.txt.gz 2012-06-11 07:51 63 netGeoFor1.sql 2012-08-19 12:01 2.1K netGeoFor1.txt.gz 2012-08-19 12:01 35M chainGeoFor1Link.sql 2012-08-19 12:01 1.6K chainGeoFor1Link.txt.gz 2012-08-19 12:02 589M chainGeoFor1.sql 2012-08-19 12:04 1.7K chainGeoFor1.txt.gz 2012-08-19 12:04 93M chainPetMar2Link.sql 2013-01-24 00:12 1.6K chainPetMar2Link.txt.gz 2013-01-24 00:12 12M netPetMar2.sql 2013-01-24 00:12 2.1K chainPetMar2.sql 2013-01-24 00:12 1.7K chainPetMar2.txt.gz 2013-01-24 00:12 2.8M netPetMar2.txt.gz 2013-01-24 00:12 2.3M cytoBandIdeo.sql 2013-04-28 15:31 1.5K cytoBandIdeo.txt.gz 2013-04-28 15:31 79K ucscToEnsembl.sql 2013-06-16 17:56 1.4K ucscToEnsembl.txt.gz 2013-06-16 17:56 99K ucscToINSDC.sql 2013-09-15 13:24 1.4K ucscToINSDC.txt.gz 2013-09-15 13:24 120K pubsBingBlat.sql 2014-01-26 12:58 2.4K pubsBingBlat.txt.gz 2014-01-26 12:58 844K pubsBingBlatPsl.sql 2014-01-26 12:58 2.2K pubsBingBlatPsl.txt.gz 2014-01-26 12:58 664K grp.sql 2014-03-02 03:41 1.3K grp.txt.gz 2014-03-02 03:41 209 snp138.sql 2014-03-09 08:44 2.9K snp138.txt.gz 2014-03-09 08:44 133M snp138CodingDbSnp.sql 2014-03-09 08:45 1.7K snp138CodingDbSnp.txt.gz 2014-03-09 08:45 2.3M snp138Common.sql 2014-03-09 08:45 3.0K snp138Common.txt.gz 2014-03-09 08:45 383K snp138ExceptionDesc.sql 2014-03-09 08:45 1.4K snp138ExceptionDesc.txt.gz 2014-03-09 08:45 1.0K snp138Mult.sql 2014-03-09 08:45 2.9K snp138Mult.txt.gz 2014-03-09 08:45 2.9M snp138Seq.sql 2014-03-09 08:45 1.3K snp138Seq.txt.gz 2014-03-09 08:45 57M chainTaeGut2.sql 2014-05-18 18:43 1.7K chainTaeGut2.txt.gz 2014-05-18 18:43 18M chainTaeGut2Link.sql 2014-05-18 18:43 1.5K chainTaeGut2Link.txt.gz 2014-05-18 18:43 222M netTaeGut2.sql 2014-05-18 18:44 2.1K netTaeGut2.txt.gz 2014-05-18 18:44 31M cpgIslandExtUnmasked.sql 2014-06-01 13:30 1.7K cpgIslandExtUnmasked.txt.gz 2014-06-01 13:30 541K animalQtl.sql 2014-06-29 20:27 1.5K animalQtl.txt.gz 2014-06-29 20:27 33K augustusGene.sql 2015-07-26 13:45 1.9K augustusGene.txt.gz 2015-07-26 13:45 1.5M microsat.sql 2015-08-23 17:01 1.5K microsat.txt.gz 2015-08-23 17:01 24K ensGtp.sql 2015-09-14 02:14 1.4K ensGtp.txt.gz 2015-09-14 02:14 187K ensPep.sql 2015-09-14 02:15 1.3K ensPep.txt.gz 2015-09-14 02:15 5.2M ensemblSource.sql 2015-09-14 02:15 1.4K ensemblSource.txt.gz 2015-09-14 02:15 56K ensemblToGeneName.sql 2015-09-14 02:15 1.4K ensemblToGeneName.txt.gz 2015-09-14 02:15 112K ensGene.sql 2015-09-14 02:15 1.9K ensGene.txt.gz 2015-09-14 02:15 1.7M chromAlias.sql 2018-02-18 06:35 1.4K chromAlias.txt.gz 2018-02-18 06:35 178K ucscToRefSeq.sql 2018-02-18 06:35 1.4K ucscToRefSeq.txt.gz 2018-02-18 06:35 132K tableDescriptions.sql 2019-07-21 03:41 1.4K tableDescriptions.txt.gz 2019-07-21 03:41 7.8K all_est.sql 2020-05-08 00:49 2.1K estOrientInfo.sql 2020-05-08 00:49 1.8K intronEst.sql 2020-05-08 00:49 2.1K estOrientInfo.txt.gz 2020-05-08 00:49 7.2M intronEst.txt.gz 2020-05-08 00:49 19M all_est.txt.gz 2020-05-08 00:49 36M all_mrna.sql 2020-08-21 19:59 2.1K all_mrna.txt.gz 2020-08-21 19:59 1.9M xenoMrna.sql 2020-08-21 19:59 2.1K xenoMrna.txt.gz 2020-08-21 19:59 173M refGene.sql 2020-08-21 20:38 1.9K refGene.txt.gz 2020-08-21 20:38 711K refFlat.sql 2020-08-21 20:38 1.7K refFlat.txt.gz 2020-08-21 20:38 663K xenoRefGene.sql 2020-08-21 20:43 1.9K xenoRefGene.txt.gz 2020-08-21 20:43 22M xenoRefFlat.sql 2020-08-21 20:43 1.7K xenoRefFlat.txt.gz 2020-08-21 20:43 20M mrnaOrientInfo.sql 2020-08-21 20:43 1.8K mrnaOrientInfo.txt.gz 2020-08-21 20:43 565K refSeqAli.sql 2020-08-21 20:58 2.1K refSeqAli.txt.gz 2020-08-21 20:58 753K xenoRefSeqAli.sql 2020-08-21 20:59 2.1K xenoRefSeqAli.txt.gz 2020-08-21 20:59 19M gbLoaded.sql 2020-08-21 21:13 1.6K gbLoaded.txt.gz 2020-08-21 21:13 44K trackDb.sql 2021-12-27 12:19 2.1K trackDb.txt.gz 2021-12-27 12:19 57K hgFindSpec.sql 2021-12-27 12:19 1.8K hgFindSpec.txt.gz 2021-12-27 12:19 1.0K tableList.sql 2023-01-22 03:11 1.6K tableList.txt.gz 2023-01-22 03:11 4.4K bigFiles.sql 2023-01-22 03:11 1.4K bigFiles.txt.gz 2023-01-22 03:11 68