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 - all_est.sql 2020-05-08 00:49 2.1K 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 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 bigFiles.sql 2021-05-09 03:10 1.4K bigFiles.txt.gz 2021-05-09 03:10 68 chainGeoFor1.sql 2012-08-19 12:04 1.7K chainGeoFor1.txt.gz 2012-08-19 12:04 93M chainGeoFor1Link.sql 2012-08-19 12:01 1.6K chainGeoFor1Link.txt.gz 2012-08-19 12:02 589M chainMm10.sql 2012-06-11 07:27 1.6K chainMm10.txt.gz 2012-06-11 07:27 7.2M chainMm10Link.sql 2012-06-11 07:47 1.5K chainMm10Link.txt.gz 2012-06-11 07:48 53M chainPetMar2.sql 2013-01-24 00:12 1.7K chainPetMar2.txt.gz 2013-01-24 00:12 2.8M chainPetMar2Link.sql 2013-01-24 00:12 1.6K chainPetMar2Link.txt.gz 2013-01-24 00:12 12M 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 chromAlias.sql 2018-02-18 06:35 1.4K chromAlias.txt.gz 2018-02-18 06:35 178K chromInfo.sql 2012-06-11 06:21 1.3K chromInfo.txt.gz 2012-06-11 06:21 78K cpgIslandExt.sql 2012-06-11 06:23 1.6K cpgIslandExt.txt.gz 2012-06-11 06:23 472K cpgIslandExtUnmasked.sql 2014-06-01 13:30 1.7K cpgIslandExtUnmasked.txt.gz 2014-06-01 13:30 541K cytoBandIdeo.sql 2013-04-28 15:31 1.5K cytoBandIdeo.txt.gz 2013-04-28 15:31 79K ensGene.sql 2015-09-14 02:15 1.9K ensGene.txt.gz 2015-09-14 02:15 1.7M 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 estOrientInfo.sql 2020-05-08 00:49 1.8K estOrientInfo.txt.gz 2020-05-08 00:49 7.2M gap.sql 2012-06-11 07:11 1.5K gap.txt.gz 2012-06-11 07:11 181K gbLoaded.sql 2020-08-21 21:13 1.6K gbLoaded.txt.gz 2020-08-21 21:13 44K gc5BaseBw.sql 2012-06-11 07:51 1.2K gc5BaseBw.txt.gz 2012-06-11 07:51 63 genscan.sql 2012-06-11 06:20 1.6K genscan.txt.gz 2012-06-11 06:20 1.4M genscanSubopt.sql 2012-06-11 06:20 1.5K genscanSubopt.txt.gz 2012-06-11 06:21 2.8M gold.sql 2012-06-11 06:20 1.6K gold.txt.gz 2012-06-11 06:20 213K grp.sql 2014-03-02 03:41 1.3K grp.txt.gz 2014-03-02 03:41 209 hgFindSpec.sql 2020-10-25 08:01 1.7K hgFindSpec.txt.gz 2020-10-25 08:01 1.0K history.sql 2012-06-11 06:20 1.5K history.txt.gz 2012-06-11 06:20 392 intronEst.sql 2020-05-08 00:49 2.1K intronEst.txt.gz 2020-05-08 00:49 19M microsat.sql 2015-08-23 17:01 1.5K microsat.txt.gz 2015-08-23 17:01 24K mrnaOrientInfo.sql 2020-08-21 20:43 1.8K mrnaOrientInfo.txt.gz 2020-08-21 20:43 565K nestedRepeats.sql 2012-06-11 07:25 1.9K nestedRepeats.txt.gz 2012-06-11 07:25 671K netGeoFor1.sql 2012-08-19 12:01 2.1K netGeoFor1.txt.gz 2012-08-19 12:01 35M netMm10.sql 2012-06-11 07:08 2.0K netMm10.txt.gz 2012-06-11 07:09 7.7M netPetMar2.sql 2013-01-24 00:12 2.1K netPetMar2.txt.gz 2013-01-24 00:12 2.3M netTaeGut2.sql 2014-05-18 18:44 2.1K netTaeGut2.txt.gz 2014-05-18 18:44 31M 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 refFlat.sql 2020-08-21 20:38 1.7K refFlat.txt.gz 2020-08-21 20:38 663K refGene.sql 2020-08-21 20:38 1.9K refGene.txt.gz 2020-08-21 20:38 711K refSeqAli.sql 2020-08-21 20:58 2.1K refSeqAli.txt.gz 2020-08-21 20:58 753K rmsk.sql 2012-06-11 07:45 1.8K rmsk.txt.gz 2012-06-11 07:45 14M simpleRepeat.sql 2012-06-11 06:21 1.9K simpleRepeat.txt.gz 2012-06-11 06:21 4.9M 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 tableDescriptions.sql 2019-07-21 03:41 1.4K tableDescriptions.txt.gz 2019-07-21 03:41 7.8K tableList.sql 2021-05-09 03:10 1.6K tableList.txt.gz 2021-05-09 03:10 4.4K trackDb.sql 2020-10-22 21:20 2.0K trackDb.txt.gz 2020-10-22 21:20 55K 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 ucscToRefSeq.sql 2018-02-18 06:35 1.4K ucscToRefSeq.txt.gz 2018-02-18 06:35 132K windowmaskerSdust.sql 2012-06-11 06:58 1.4K windowmaskerSdust.txt.gz 2012-06-11 06:59 54M xenoMrna.sql 2020-08-21 19:59 2.1K xenoMrna.txt.gz 2020-08-21 19:59 173M xenoRefFlat.sql 2020-08-21 20:43 1.7K xenoRefFlat.txt.gz 2020-08-21 20:43 20M xenoRefGene.sql 2020-08-21 20:43 1.9K xenoRefGene.txt.gz 2020-08-21 20:43 22M xenoRefSeqAli.sql 2020-08-21 20:59 2.1K xenoRefSeqAli.txt.gz 2020-08-21 20:59 19M