This directory contains a dump of the UCSC genome annotation database for
the June 2007 assembly of the marmoset genome (calJac1,
Callithrix_jacchus-WUSTL 2.0.2). The annotations were generated by UCSC
and collaborators worldwide.
This assembly was produced by the Genome Sequencing Center at the Washington
University School of Medicine in St. Louis. For more information on the
marmoset genome, see the project website:
http://genome.wustl.edu/genome.cgi?GENOME=Callithrix%20jacchus
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=calJac1
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/calJac1/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/calJac1/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/calJac1/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/calJac1/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/calJac1/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 calJac1 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql calJac1 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
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The Marmoset 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.
It is requested that users of this marmoset sequence assembly acknowledge
the Washington University School of Medicine, Genome Sequencing Center
in any publications that result from use of this sequence assembly.
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.
All the files and tables in this directory are freely usable for any purpose.
Name Last modified Size Description
Parent Directory -
xenoRefSeqAli.txt.gz 2020-08-21 00:22 41M
xenoRefSeqAli.sql 2020-08-21 00:22 2.1K
xenoRefGene.txt.gz 2020-08-21 00:22 37M
xenoRefGene.sql 2020-08-21 00:22 2.0K
xenoRefFlat.txt.gz 2020-08-21 00:22 33M
xenoRefFlat.sql 2020-08-21 00:22 1.7K
xenoMrna.txt.gz 2016-02-21 11:03 351M
xenoMrna.sql 2016-02-21 11:02 2.3K
trackDb.txt.gz 2023-03-28 13:46 33K
trackDb.sql 2023-03-28 13:46 2.1K
tableList.txt.gz 2024-12-08 03:14 3.9K
tableList.sql 2024-12-08 03:14 1.6K
tableDescriptions.txt.gz 2024-12-07 02:03 5.5K
tableDescriptions.sql 2024-12-07 02:03 1.5K
simpleRepeat.txt.gz 2008-04-23 13:08 25M
simpleRepeat.sql 2008-04-23 13:07 1.9K
rmsk.txt.gz 2008-04-23 13:06 130M
rmsk.sql 2008-04-23 13:05 1.9K
refSeqAli.txt.gz 2020-08-21 00:22 22K
refSeqAli.sql 2020-08-21 00:22 2.1K
refGene.txt.gz 2020-08-21 00:22 19K
refGene.sql 2020-08-21 00:22 1.9K
refFlat.txt.gz 2020-08-21 00:22 18K
refFlat.sql 2020-08-21 00:22 1.7K
quality.txt.gz 2008-11-30 07:36 59M
quality.sql 2008-11-30 07:35 1.7K
phastConsElements9way.txt.gz 2008-04-23 13:04 12M
phastConsElements9way.sql 2008-04-23 13:04 1.4K
phastCons9way.txt.gz 2008-04-23 13:03 78M
phastCons9way.sql 2008-04-23 13:01 1.7K
nscanPep.txt.gz 2008-04-23 13:01 7.7M
nscanPep.sql 2008-04-23 13:01 1.1K
nscanGene.txt.gz 2008-04-23 13:01 2.3M
nscanGene.sql 2008-04-23 13:01 1.9K
netRheMac2.txt.gz 2008-04-23 13:00 51M
netRheMac2.sql 2008-04-23 12:59 2.2K
netPonAbe2.txt.gz 2008-04-23 12:59 52M
netPonAbe2.sql 2008-04-23 12:58 2.2K
netPanTro2.txt.gz 2008-04-23 12:57 50M
netPanTro2.sql 2008-04-23 12:56 2.2K
netOrnAna1.txt.gz 2008-04-23 12:56 18M
netOrnAna1.sql 2008-04-23 12:55 2.2K
netMonDom4.txt.gz 2008-04-23 12:55 30M
netMonDom4.sql 2008-04-23 12:55 2.2K
netMm9.txt.gz 2008-04-23 12:54 73M
netMm9.sql 2008-04-23 12:52 2.2K
netHg19.txt.gz 2009-07-26 06:29 41M
netHg19.sql 2009-07-26 06:29 2.3K
netCanFam2.txt.gz 2008-04-23 12:50 80M
netCanFam2.sql 2008-04-23 12:49 2.2K
multiz9waySummary.txt.gz 2008-04-23 12:49 1.5M
multiz9waySummary.sql 2008-04-23 12:49 1.5K
multiz9wayFrames.txt.gz 2008-04-23 12:48 20M
multiz9wayFrames.sql 2008-04-23 12:48 1.6K
multiz9way.txt.gz 2008-04-23 12:47 127M
multiz9way.sql 2008-04-23 12:45 1.4K
mrnaOrientInfo.txt.gz 2020-08-21 00:22 23K
mrnaOrientInfo.sql 2020-08-21 00:22 1.8K
microsat.txt.gz 2015-08-23 11:15 467K
microsat.sql 2015-08-23 11:15 1.5K
intronEst.txt.gz 2016-06-05 09:13 7.9M
intronEst.sql 2016-06-05 09:13 2.1K
history.txt.gz 2008-04-23 12:44 901
history.sql 2008-04-23 12:44 1.4K
hgFindSpec.txt.gz 2023-03-28 13:46 621
hgFindSpec.sql 2023-03-28 13:46 1.8K
grp.txt.gz 2014-03-02 03:40 208
grp.sql 2014-03-02 03:40 1.4K
gold.txt.gz 2008-04-23 12:44 4.0M
gold.sql 2008-04-23 12:44 1.6K
genscanSubopt.txt.gz 2008-04-23 12:44 6.9M
genscanSubopt.sql 2008-04-23 12:44 1.5K
genscanPep.txt.gz 2008-04-23 12:44 11M
genscanPep.sql 2008-04-23 12:44 1.2K
genscan.txt.gz 2008-04-23 12:44 3.0M
genscan.sql 2008-04-23 12:44 1.6K
gc5Base.txt.gz 2008-04-23 12:44 13M
gc5Base.sql 2008-04-23 12:44 1.7K
gbLoaded.txt.gz 2020-08-21 00:22 43K
gbLoaded.sql 2020-08-21 00:22 1.6K
gap.txt.gz 2008-04-23 12:42 2.6M
gap.sql 2008-04-23 12:42 1.5K
extFile.txt.gz 2008-04-23 12:42 121
extFile.sql 2008-04-23 12:42 1.3K
estOrientInfo.txt.gz 2016-06-05 09:13 3.4M
estOrientInfo.sql 2016-06-05 09:13 1.8K
chromInfo.txt.gz 2008-04-23 12:42 258K
chromInfo.sql 2008-04-23 12:42 1.2K
chainRheMac2Link.txt.gz 2008-04-23 12:32 674M
chainRheMac2Link.sql 2008-04-23 12:24 1.4K
chainRheMac2.txt.gz 2008-04-23 12:23 140M
chainRheMac2.sql 2008-04-23 12:21 1.7K
chainPonAbe2Link.txt.gz 2008-04-23 12:05 1.0G
chainPonAbe2Link.sql 2008-04-23 11:52 1.4K
chainPonAbe2.txt.gz 2008-04-23 11:48 289M
chainPonAbe2.sql 2008-04-23 11:44 1.7K
chainPanTro2Link.txt.gz 2008-04-23 11:29 1.0G
chainPanTro2Link.sql 2008-04-23 11:17 1.4K
chainPanTro2.txt.gz 2008-04-23 11:13 291M
chainPanTro2.sql 2008-04-23 11:10 1.7K
chainOrnAna1Link.txt.gz 2008-04-23 11:07 179M
chainOrnAna1Link.sql 2008-04-23 11:04 1.4K
chainOrnAna1.txt.gz 2008-04-23 11:04 39M
chainOrnAna1.sql 2008-04-23 11:03 1.7K
chainMonDom4Link.txt.gz 2008-04-22 14:36 1.4G
chainMonDom4Link.sql 2008-04-22 14:08 1.5K
chainMonDom4.txt.gz 2008-04-22 14:02 420M
chainMonDom4.sql 2008-04-22 13:56 1.7K
chainMm9Link.txt.gz 2008-04-22 13:47 485M
chainMm9Link.sql 2008-04-22 13:41 1.4K
chainMm9.txt.gz 2008-04-22 13:40 66M
chainMm9.sql 2008-04-22 13:39 1.6K
chainHg19Link.txt.gz 2009-07-26 06:27 240M
chainHg19Link.sql 2009-07-26 06:27 1.5K
chainHg19.txt.gz 2009-07-26 06:27 16M
chainHg19.sql 2009-07-26 06:27 1.8K
chainCanFam2Link.txt.gz 2008-04-22 12:45 504M
chainCanFam2Link.sql 2008-04-22 12:36 1.4K
chainCanFam2.txt.gz 2008-04-22 12:36 43M
chainCanFam2.sql 2008-04-22 12:35 1.7K
bigFiles.txt.gz 2024-12-08 03:14 33
bigFiles.sql 2024-12-08 03:14 1.4K
augustusGene.txt.gz 2015-07-26 10:46 2.3M
augustusGene.sql 2015-07-26 10:46 1.9K
all_mrna.txt.gz 2020-05-07 13:34 76K
all_mrna.sql 2020-05-07 13:34 2.1K
all_est.txt.gz 2016-06-05 09:13 11M
all_est.sql 2016-06-05 09:13 2.1K