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 -
chainMonDom4Link.txt.gz 2008-04-22 14:36 1.4G
chainPonAbe2Link.txt.gz 2008-04-23 12:05 1.0G
chainPanTro2Link.txt.gz 2008-04-23 11:29 1.0G
chainRheMac2Link.txt.gz 2008-04-23 12:32 674M
chainCanFam2Link.txt.gz 2008-04-22 12:45 504M
chainMm9Link.txt.gz 2008-04-22 13:47 485M
chainMonDom4.txt.gz 2008-04-22 14:02 420M
xenoMrna.txt.gz 2016-02-21 11:03 351M
chainPanTro2.txt.gz 2008-04-23 11:13 291M
chainPonAbe2.txt.gz 2008-04-23 11:48 289M
chainHg19Link.txt.gz 2009-07-26 06:27 240M
chainOrnAna1Link.txt.gz 2008-04-23 11:07 179M
chainRheMac2.txt.gz 2008-04-23 12:23 140M
rmsk.txt.gz 2008-04-23 13:06 130M
multiz9way.txt.gz 2008-04-23 12:47 127M
netCanFam2.txt.gz 2008-04-23 12:50 80M
phastCons9way.txt.gz 2008-04-23 13:03 78M
netMm9.txt.gz 2008-04-23 12:54 73M
chainMm9.txt.gz 2008-04-22 13:40 66M
quality.txt.gz 2008-11-30 07:36 59M
netPonAbe2.txt.gz 2008-04-23 12:59 52M
netRheMac2.txt.gz 2008-04-23 13:00 51M
netPanTro2.txt.gz 2008-04-23 12:57 50M
chainCanFam2.txt.gz 2008-04-22 12:36 43M
netHg19.txt.gz 2009-07-26 06:29 41M
xenoRefSeqAli.txt.gz 2020-08-21 00:22 41M
chainOrnAna1.txt.gz 2008-04-23 11:04 39M
xenoRefGene.txt.gz 2020-08-21 00:22 37M
xenoRefFlat.txt.gz 2020-08-21 00:22 33M
netMonDom4.txt.gz 2008-04-23 12:55 30M
simpleRepeat.txt.gz 2008-04-23 13:08 25M
multiz9wayFrames.txt.gz 2008-04-23 12:48 20M
netOrnAna1.txt.gz 2008-04-23 12:56 18M
chainHg19.txt.gz 2009-07-26 06:27 16M
gc5Base.txt.gz 2008-04-23 12:44 13M
phastConsElements9way.txt.gz 2008-04-23 13:04 12M
genscanPep.txt.gz 2008-04-23 12:44 11M
all_est.txt.gz 2016-06-05 09:13 11M
intronEst.txt.gz 2016-06-05 09:13 7.9M
nscanPep.txt.gz 2008-04-23 13:01 7.7M
genscanSubopt.txt.gz 2008-04-23 12:44 6.9M
gold.txt.gz 2008-04-23 12:44 4.0M
estOrientInfo.txt.gz 2016-06-05 09:13 3.4M
genscan.txt.gz 2008-04-23 12:44 3.0M
gap.txt.gz 2008-04-23 12:42 2.6M
nscanGene.txt.gz 2008-04-23 13:01 2.3M
augustusGene.txt.gz 2015-07-26 10:46 2.3M
multiz9waySummary.txt.gz 2008-04-23 12:49 1.5M
microsat.txt.gz 2015-08-23 11:15 467K
chromInfo.txt.gz 2008-04-23 12:42 258K
all_mrna.txt.gz 2020-05-07 13:34 76K
gbLoaded.txt.gz 2020-08-21 00:22 43K
trackDb.txt.gz 2023-03-28 13:46 33K
mrnaOrientInfo.txt.gz 2020-08-21 00:22 23K
refSeqAli.txt.gz 2020-08-21 00:22 22K
refGene.txt.gz 2020-08-21 00:22 19K
refFlat.txt.gz 2020-08-21 00:22 18K
tableDescriptions.txt.gz 2024-11-16 02:03 5.5K
tableList.txt.gz 2024-11-17 03:21 3.9K
xenoMrna.sql 2016-02-21 11:02 2.3K
netHg19.sql 2009-07-26 06:29 2.3K
netRheMac2.sql 2008-04-23 12:59 2.2K
netPonAbe2.sql 2008-04-23 12:58 2.2K
netPanTro2.sql 2008-04-23 12:56 2.2K
netOrnAna1.sql 2008-04-23 12:55 2.2K
netMonDom4.sql 2008-04-23 12:55 2.2K
netCanFam2.sql 2008-04-23 12:49 2.2K
netMm9.sql 2008-04-23 12:52 2.2K
xenoRefSeqAli.sql 2020-08-21 00:22 2.1K
refSeqAli.sql 2020-08-21 00:22 2.1K
all_mrna.sql 2020-05-07 13:34 2.1K
intronEst.sql 2016-06-05 09:13 2.1K
all_est.sql 2016-06-05 09:13 2.1K
trackDb.sql 2023-03-28 13:46 2.1K
xenoRefGene.sql 2020-08-21 00:22 2.0K
refGene.sql 2020-08-21 00:22 1.9K
augustusGene.sql 2015-07-26 10:46 1.9K
simpleRepeat.sql 2008-04-23 13:07 1.9K
nscanGene.sql 2008-04-23 13:01 1.9K
rmsk.sql 2008-04-23 13:05 1.9K
mrnaOrientInfo.sql 2020-08-21 00:22 1.8K
chainHg19.sql 2009-07-26 06:27 1.8K
estOrientInfo.sql 2016-06-05 09:13 1.8K
hgFindSpec.sql 2023-03-28 13:46 1.8K
xenoRefFlat.sql 2020-08-21 00:22 1.7K
phastCons9way.sql 2008-04-23 13:01 1.7K
refFlat.sql 2020-08-21 00:22 1.7K
quality.sql 2008-11-30 07:35 1.7K
gc5Base.sql 2008-04-23 12:44 1.7K
chainRheMac2.sql 2008-04-23 12:21 1.7K
chainPonAbe2.sql 2008-04-23 11:44 1.7K
chainPanTro2.sql 2008-04-23 11:10 1.7K
chainOrnAna1.sql 2008-04-23 11:03 1.7K
chainMonDom4.sql 2008-04-22 13:56 1.7K
chainCanFam2.sql 2008-04-22 12:35 1.7K
chainMm9.sql 2008-04-22 13:39 1.6K
gbLoaded.sql 2020-08-21 00:22 1.6K
gold.sql 2008-04-23 12:44 1.6K
genscan.sql 2008-04-23 12:44 1.6K
tableList.sql 2024-11-17 03:21 1.6K
multiz9wayFrames.sql 2008-04-23 12:48 1.6K
chainHg19Link.sql 2009-07-26 06:27 1.5K
gap.sql 2008-04-23 12:42 1.5K
microsat.sql 2015-08-23 11:15 1.5K
chainMonDom4Link.sql 2008-04-22 14:08 1.5K
multiz9waySummary.sql 2008-04-23 12:49 1.5K
genscanSubopt.sql 2008-04-23 12:44 1.5K
phastConsElements9way.sql 2008-04-23 13:04 1.4K
tableDescriptions.sql 2024-11-16 02:03 1.4K
history.sql 2008-04-23 12:44 1.4K
chainRheMac2Link.sql 2008-04-23 12:24 1.4K
chainPonAbe2Link.sql 2008-04-23 11:52 1.4K
chainPanTro2Link.sql 2008-04-23 11:17 1.4K
chainOrnAna1Link.sql 2008-04-23 11:04 1.4K
chainCanFam2Link.sql 2008-04-22 12:36 1.4K
multiz9way.sql 2008-04-23 12:45 1.4K
chainMm9Link.sql 2008-04-22 13:41 1.4K
grp.sql 2014-03-02 03:40 1.4K
bigFiles.sql 2024-11-17 03:21 1.4K
extFile.sql 2008-04-23 12:42 1.3K
chromInfo.sql 2008-04-23 12:42 1.2K
genscanPep.sql 2008-04-23 12:44 1.2K
nscanPep.sql 2008-04-23 13:01 1.1K
history.txt.gz 2008-04-23 12:44 901
hgFindSpec.txt.gz 2023-03-28 13:46 621
grp.txt.gz 2014-03-02 03:40 208
extFile.txt.gz 2008-04-23 12:42 121
bigFiles.txt.gz 2024-11-17 03:21 33