This directory contains a dump of the UCSC genome annotation database for the
    Oct. 2014 (aquChr-1.0.2/aquChr2) assembly of the golden eagle genome
    (aquChr2, WashU) .

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/32031
    http://www.ncbi.nlm.nih.gov/genome/assembly/217061
    http://www.ncbi.nlm.nih.gov/bioproject/256103

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=aquChr2
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/aquChr2/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/aquChr2/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/aquChr2/database/gc5BaseBw.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/aquChr2/database/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/aquChr2/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 aquChr2 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql aquChr2 --local-infile=1 
        -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'

The Golden eagle 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 acknowledged.  See
   http://genome.ucsc.edu/goldenPath/credits.html for credit information.

3. The centers producing the data reserve the right to publish the initial
   large-scale analyses of the data set, 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 chromosome (that
   is, 30 Mb or more).

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

-----------------------------------------------------------------------------
GenBank Data Usage

The GenBank database is designed to provide and encourage access within
the scientific community to the most up to date and comprehensive DNA
sequence information. Therefore, NCBI places no restrictions on the use
or distribution of the GenBank data. However, some submitters may claim
patent, copyright, or other intellectual property rights in all or a
portion of the data they have submitted. NCBI is not in a position to
assess the validity of such claims, and therefore cannot provide comment
or unrestricted permission concerning the use, copying, or distribution
of the information contained in GenBank.
-----------------------------------------------------------------------------
All the files and tables in this directory are freely usable for any purpose.

      Name                        Last modified      Size  Description
Parent Directory - gbWarn.txt.gz 2017-05-11 14:43 31 imageClone.txt.gz 2017-05-11 14:08 35 sex.txt.gz 2017-05-11 14:44 39 cell.txt.gz 2017-05-11 14:09 40 library.txt.gz 2017-05-11 14:09 43 development.txt.gz 2017-05-11 14:44 47 tissue.txt.gz 2017-05-11 14:44 59 gc5BaseBw.txt.gz 2017-05-11 14:43 66 bigFiles.txt.gz 2024-02-25 03:10 69 grp.txt.gz 2017-05-11 14:44 213 keyword.txt.gz 2017-05-11 14:08 486 hgFindSpec_pushedout.txt.gz 2021-08-02 14:26 546 hgFindSpec.txt.gz 2023-03-28 13:46 586 history.txt.gz 2017-05-11 14:44 655 gbExtFile.txt.gz 2017-05-11 14:09 1.1K gc5BaseBw.sql 2017-05-11 14:43 1.3K gbWarn.sql 2017-05-11 14:43 1.3K grp.sql 2017-05-11 14:44 1.3K mrnaClone.txt.gz 2017-05-11 14:43 1.4K bigFiles.sql 2024-02-25 03:10 1.4K chromInfo.sql 2017-05-11 14:44 1.4K cds.sql 2017-05-11 14:08 1.4K sex.sql 2017-05-11 14:44 1.4K cell.sql 2017-05-11 14:09 1.4K author.sql 2017-05-11 14:08 1.4K source.sql 2017-05-11 14:44 1.4K tissue.sql 2017-05-11 14:44 1.4K gbExtFile.sql 2017-05-11 14:09 1.4K keyword.sql 2017-05-11 14:08 1.4K library.sql 2017-05-11 14:09 1.4K geneName.sql 2017-05-11 14:44 1.4K organism.sql 2017-05-11 14:44 1.4K mrnaClone.sql 2017-05-11 14:43 1.4K description.sql 2017-05-11 14:44 1.4K development.sql 2017-05-11 14:44 1.4K productName.sql 2017-05-11 14:44 1.4K chromAlias.sql 2017-05-11 14:44 1.4K ucscToINSDC.sql 2017-05-11 14:44 1.4K tableDescriptions.sql 2024-02-24 02:03 1.4K ucscToRefSeq.sql 2017-05-11 14:44 1.4K gbMiscDiff.txt.gz 2017-05-11 14:44 1.5K gbMiscDiff.sql 2017-05-11 14:44 1.5K microsat.sql 2017-05-11 14:43 1.5K refSeqSummary.sql 2017-05-11 14:44 1.5K imageClone.sql 2017-05-11 14:08 1.5K windowmaskerSdust.sql 2017-05-11 14:44 1.5K cytoBandIdeo.sql 2017-05-11 14:44 1.5K chainHg38Link.sql 2017-05-11 14:43 1.5K chainMm10Link.sql 2017-05-11 14:43 1.5K chainGalGal5Link.sql 2017-05-11 14:13 1.5K chainGalGal6Link.sql 2019-01-20 07:56 1.5K tableList.sql 2024-02-25 03:10 1.6K history.sql 2017-05-11 14:44 1.6K gap.sql 2017-05-11 14:44 1.6K refSeqStatus.sql 2017-05-11 14:44 1.6K gbLoaded.sql 2020-08-18 07:06 1.6K gold.sql 2017-05-11 14:44 1.7K genscan.sql 2017-05-11 14:44 1.7K cpgIslandExt.sql 2017-05-11 14:44 1.7K chainHg38.sql 2017-05-11 14:43 1.7K chainMm10.sql 2017-05-11 14:43 1.7K gbSeq.sql 2017-05-11 14:09 1.7K chainGalGal5.sql 2017-05-11 14:09 1.7K chainGalGal6.sql 2019-01-20 07:55 1.7K cpgIslandExtUnmasked.sql 2017-05-11 14:44 1.7K refLink.sql 2017-05-11 14:44 1.7K xenoRefFlat.sql 2020-08-18 07:06 1.7K hgFindSpec.sql 2023-03-28 13:46 1.8K hgFindSpec_pushedout.sql 2021-08-02 14:26 1.8K rmsk.sql 2017-05-11 14:44 1.9K gbStatus.sql 2017-05-11 14:13 1.9K simpleRepeat.sql 2017-05-11 14:44 1.9K nestedRepeats.sql 2017-05-11 14:44 1.9K augustusGene.sql 2017-05-11 14:08 1.9K xenoRefGene.sql 2020-08-18 07:06 2.0K trackDb.sql 2023-03-28 13:46 2.1K trackDb_pushedout.sql 2021-08-02 14:26 2.1K netHg38.sql 2017-05-11 14:44 2.1K netMm10.sql 2017-05-11 14:44 2.1K netGalGal5.sql 2017-05-11 14:44 2.1K netGalGal6.sql 2019-01-20 08:06 2.1K xenoRefSeqAli.sql 2020-08-18 07:06 2.1K gbCdnaInfo.sql 2017-05-11 14:08 2.6K tableList.txt.gz 2024-02-25 03:10 3.4K gbLoaded.txt.gz 2020-08-18 07:06 5.4K cytoBandIdeo.txt.gz 2017-05-11 14:44 6.6K tableDescriptions.txt.gz 2024-02-24 02:03 7.1K chromInfo.txt.gz 2017-05-11 14:44 7.4K ucscToINSDC.txt.gz 2017-05-11 14:44 9.2K ucscToRefSeq.txt.gz 2017-05-11 14:44 9.3K chromAlias.txt.gz 2017-05-11 14:44 11K microsat.txt.gz 2017-05-11 14:43 16K trackDb_pushedout.txt.gz 2021-08-02 14:26 33K trackDb.txt.gz 2023-03-28 13:46 37K gap.txt.gz 2017-05-11 14:44 220K organism.txt.gz 2017-05-11 14:44 267K source.txt.gz 2017-05-11 14:44 273K gold.txt.gz 2017-05-11 14:44 294K nestedRepeats.txt.gz 2017-05-11 14:44 404K cpgIslandExt.txt.gz 2017-05-11 14:44 752K cpgIslandExtUnmasked.txt.gz 2017-05-11 14:44 843K augustusGene.txt.gz 2017-05-11 14:08 1.5M refSeqStatus.txt.gz 2017-05-11 14:44 1.5M genscan.txt.gz 2017-05-11 14:44 1.6M cds.txt.gz 2017-05-11 14:08 1.9M geneName.txt.gz 2017-05-11 14:44 2.3M productName.txt.gz 2017-05-11 14:44 2.7M author.txt.gz 2017-05-11 14:08 3.1M gbStatus.txt.gz 2017-05-11 14:13 3.6M simpleRepeat.txt.gz 2017-05-11 14:44 4.2M refSeqSummary.txt.gz 2017-05-11 14:44 5.8M chainMm10.txt.gz 2017-05-11 14:43 6.4M gbCdnaInfo.txt.gz 2017-05-11 14:08 7.9M netMm10.txt.gz 2017-05-11 14:44 8.1M description.txt.gz 2017-05-11 14:44 8.4M netHg38.txt.gz 2017-05-11 14:44 11M refLink.txt.gz 2017-05-11 14:44 11M rmsk.txt.gz 2017-05-11 14:44 12M gbSeq.txt.gz 2017-05-11 14:09 12M chainHg38.txt.gz 2017-05-11 14:43 16M xenoRefSeqAli.txt.gz 2020-08-18 07:06 25M xenoRefFlat.txt.gz 2020-08-18 07:06 26M xenoRefGene.txt.gz 2020-08-18 07:06 29M netGalGal5.txt.gz 2017-05-11 14:44 38M netGalGal6.txt.gz 2019-01-20 08:06 42M chainMm10Link.txt.gz 2017-05-11 14:43 55M windowmaskerSdust.txt.gz 2017-05-11 14:44 65M chainGalGal5.txt.gz 2017-05-11 14:10 70M chainHg38Link.txt.gz 2017-05-11 14:43 139M chainGalGal6.txt.gz 2019-01-20 07:55 321M chainGalGal5Link.txt.gz 2017-05-11 14:23 539M chainGalGal6Link.txt.gz 2019-01-20 07:58 2.0G