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.
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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.
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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.
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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 2024-11-17 03:15 69
grp.txt.gz 2017-05-11 14:44 213
keyword.txt.gz 2017-05-11 14:08 486
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 2024-11-17 03:15 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 2024-11-16 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 2024-11-17 03:15 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
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
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 2024-11-17 03:15 3.2K
gbLoaded.txt.gz 2020-08-18 07:06 5.4K
cytoBandIdeo.txt.gz 2017-05-11 14:44 6.6K
tableDescriptions.txt.gz 2024-11-16 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.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