This directory contains a dump of the UCSC genome annotation database for
the March 2009 (WUGSC 3.2/calJac3) assembly of
the marmoset genome (calJac3, WUSTL 3.2 (GCA_000004665.1)),
The annotations were generated by UCSC and collaborators worldwide.
This assembly was produced by the Washington University St. Louis (WUSTL)
School of Medicine Genome Sequencing Center in St. Louis.
For more information on the marmoset genome, see the project website:
For more information on the marmoset genome, see the project website:
http://genome.wustl.edu/genomes/view/callithrix_jacchus/
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=calJac3
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/calJac3/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/calJac3/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/calJac3/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/calJac3/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/calJac3/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 calJac3 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql calJac3 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
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.
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 -
chainMm9.sql 2010-05-28 13:53 1.6K
chainMm9.txt.gz 2010-05-28 13:54 57M
netMonDom5.sql 2010-05-28 13:57 2.0K
netMonDom5.txt.gz 2010-05-28 13:57 18M
rmsk.sql 2010-05-28 13:57 1.8K
rmsk.txt.gz 2010-05-28 13:57 129M
nscanPep.sql 2010-05-28 13:58 1.3K
nscanPep.txt.gz 2010-05-28 13:58 6.1M
chainHg19Link.sql 2010-05-28 13:58 1.5K
chainHg19Link.txt.gz 2010-05-28 13:59 235M
chainHg19.sql 2010-05-28 14:00 1.6K
chainHg19.txt.gz 2010-05-28 14:00 14M
netCanFam2.sql 2010-05-28 14:00 2.0K
netCanFam2.txt.gz 2010-05-28 14:01 73M
simpleRepeat.sql 2010-05-28 14:02 1.9K
simpleRepeat.txt.gz 2010-05-28 14:03 21M
netPonAbe2.sql 2010-05-28 14:03 2.0K
netPonAbe2.txt.gz 2010-05-28 14:03 40M
cpgIslandExt.sql 2010-05-28 14:03 1.6K
cpgIslandExt.txt.gz 2010-05-28 14:03 720K
ctgPos2.sql 2010-05-28 14:03 1.5K
ctgPos2.txt.gz 2010-05-28 14:03 35K
history.sql 2010-05-28 14:04 1.5K
history.txt.gz 2010-05-28 14:04 1.0K
chainMonDom5.sql 2010-05-28 14:06 1.6K
chainMonDom5.txt.gz 2010-05-28 14:07 265M
netHg19.sql 2010-05-28 14:08 2.0K
netHg19.txt.gz 2010-05-28 14:09 37M
chainCanFam2Link.sql 2010-05-28 14:09 1.5K
chainCanFam2Link.txt.gz 2010-05-28 14:10 490M
gc5Base.sql 2010-05-28 14:13 1.7K
gc5Base.txt.gz 2010-05-28 14:13 12M
nscanGene.sql 2010-05-28 14:14 1.9K
nscanGene.txt.gz 2010-05-28 14:14 2.1M
chainMonDom5Link.sql 2010-05-28 14:14 1.5K
chainMonDom5Link.txt.gz 2010-05-28 14:16 741M
chainCanFam2.sql 2010-05-28 14:22 1.6K
chainCanFam2.txt.gz 2010-05-28 14:22 39M
chainPonAbe2Link.sql 2010-05-28 14:23 1.5K
chainPonAbe2Link.txt.gz 2010-05-28 14:23 249M
chromInfo.sql 2010-05-28 14:25 1.3K
chromInfo.txt.gz 2010-05-28 14:25 85K
nestedRepeats.sql 2010-05-28 14:25 1.9K
nestedRepeats.txt.gz 2010-05-28 14:25 16M
chainMm9Link.sql 2010-05-28 14:26 1.5K
chainMm9Link.txt.gz 2010-05-28 14:27 460M
gap.sql 2010-05-28 14:31 1.5K
gap.txt.gz 2010-05-28 14:31 2.5M
chainPonAbe2.sql 2010-05-28 14:31 1.6K
chainPonAbe2.txt.gz 2010-05-28 14:31 17M
netMm9.sql 2010-05-30 13:34 2.0K
netMm9.txt.gz 2010-05-30 13:35 67M
gold.sql 2010-10-24 13:31 1.6K
gold.txt.gz 2010-10-24 13:31 3.4M
bacEndCalJac3Singles.sql 2010-10-31 13:39 1.5K
bacEndCalJac3Singles.txt.gz 2010-10-31 13:39 907K
bacEnds.sql 2010-10-31 13:39 1.7K
bacEnds.txt.gz 2010-10-31 13:39 2.2M
qualityBw.sql 2010-11-07 14:12 1.2K
qualityBw.txt.gz 2010-11-07 14:12 61
netPanTro3.sql 2011-05-23 07:58 2.0K
netPanTro3.txt.gz 2011-05-23 07:58 38M
chainPanTro3.sql 2011-05-23 07:59 1.6K
chainPanTro3.txt.gz 2011-05-23 07:59 15M
chainPanTro3Link.sql 2011-05-23 07:59 1.5K
chainPanTro3Link.txt.gz 2011-05-23 08:01 231M
extFile.sql 2011-10-24 16:01 1.4K
extFile.txt.gz 2011-10-24 16:01 104
multiz13waySummary.sql 2011-10-24 16:02 1.5K
multiz13waySummary.txt.gz 2011-10-24 16:02 28M
multiz13wayFrames.sql 2011-10-24 16:03 1.7K
multiz13wayFrames.txt.gz 2011-10-24 16:04 20M
multiz13way.sql 2011-10-24 16:05 1.5K
multiz13way.txt.gz 2011-10-24 16:07 198M
phastConsElements13way.sql 2011-10-24 16:13 1.5K
phastConsElements13way.txt.gz 2011-10-24 16:13 16M
phastCons13way.sql 2011-10-24 16:14 1.7K
phastCons13way.txt.gz 2011-10-24 16:15 73M
phyloP13wayAll.sql 2011-10-24 16:17 1.7K
phyloP13wayAll.txt.gz 2011-10-24 16:18 83M
chainGorGor3.sql 2011-11-27 08:05 1.6K
chainGorGor3.txt.gz 2011-11-27 08:05 13M
netGorGor3.sql 2011-11-27 08:06 2.0K
netGorGor3.txt.gz 2011-11-27 08:06 38M
chainGorGor3Link.sql 2011-11-27 08:06 1.5K
chainGorGor3Link.txt.gz 2011-11-27 08:06 215M
tRNAs.sql 2012-04-15 16:35 1.7K
tRNAs.txt.gz 2012-04-15 16:35 9.8K
chainMm10.sql 2012-05-07 08:57 1.6K
chainMm10.txt.gz 2012-05-07 08:58 64M
netMm10.sql 2012-05-07 08:59 2.0K
netMm10.txt.gz 2012-05-07 09:01 67M
chainMm10Link.sql 2012-05-07 09:03 1.5K
chainMm10Link.txt.gz 2012-05-07 09:07 484M
chainMicMur1.sql 2012-11-11 09:27 1.7K
chainMicMur1.txt.gz 2012-11-11 09:27 209M
chainMicMur1Link.sql 2012-11-11 09:28 1.6K
chainMicMur1Link.txt.gz 2012-11-11 09:29 688M
netMicMur1.sql 2012-11-11 09:31 2.1K
netMicMur1.txt.gz 2012-11-11 09:31 68M
chainPapHam1.sql 2012-11-18 11:15 1.7K
chainPapHam1.txt.gz 2012-11-18 11:15 17M
chainPapHam1Link.sql 2012-11-18 11:15 1.6K
chainPapHam1Link.txt.gz 2012-11-18 11:16 215M
netPapHam1.sql 2012-11-18 11:16 2.1K
netPapHam1.txt.gz 2012-11-18 11:16 45M
chainRheMac3Link.sql 2012-12-02 11:11 1.6K
chainRheMac3Link.txt.gz 2012-12-02 11:11 219M
netRheMac3.sql 2012-12-02 11:12 2.1K
netRheMac3.txt.gz 2012-12-02 11:12 42M
chainRheMac3.sql 2012-12-02 11:13 1.7K
chainRheMac3.txt.gz 2012-12-02 11:13 13M
cytoBandIdeo.sql 2013-04-28 11:15 1.5K
cytoBandIdeo.txt.gz 2013-04-28 11:15 81K
ucscToINSDC.sql 2013-09-15 09:31 1.4K
ucscToINSDC.txt.gz 2013-09-15 09:31 116K
genscan.sql 2013-12-09 19:32 1.7K
genscan.txt.gz 2013-12-09 19:32 3.1M
grp.sql 2014-03-02 03:40 1.3K
grp.txt.gz 2014-03-02 03:40 208
cpgIslandExtUnmasked.sql 2014-06-01 09:24 1.7K
cpgIslandExtUnmasked.txt.gz 2014-06-01 09:24 788K
ucscToEnsembl.sql 2014-10-19 08:20 1.4K
ucscToEnsembl.txt.gz 2014-10-19 08:20 75K
chainTarSyr2.sql 2015-05-24 21:04 1.7K
chainTarSyr2.txt.gz 2015-05-24 21:05 264M
chainTarSyr2Link.sql 2015-05-24 21:05 1.5K
chainTarSyr2Link.txt.gz 2015-05-24 21:07 1.1G
netTarSyr2.sql 2015-05-24 21:11 2.1K
netTarSyr2.txt.gz 2015-05-24 21:11 67M
augustusGene.sql 2015-07-26 10:54 1.9K
augustusGene.txt.gz 2015-07-26 10:54 2.3M
microsat.sql 2015-08-23 11:23 1.5K
microsat.txt.gz 2015-08-23 11:23 450K
estOrientInfo.sql 2016-06-12 06:19 1.8K
estOrientInfo.txt.gz 2016-06-12 06:19 3.5M
intronEst.sql 2016-06-12 06:19 2.1K
intronEst.txt.gz 2016-06-12 06:19 8.4M
all_est.sql 2016-06-12 06:20 2.1K
all_est.txt.gz 2016-06-12 06:20 11M
ensemblSource.sql 2016-11-20 05:54 1.4K
ensemblSource.txt.gz 2016-11-20 05:54 177K
ensGtp.sql 2016-11-20 05:58 1.4K
ensGtp.txt.gz 2016-11-20 05:58 512K
ensGene.sql 2016-11-20 05:59 1.9K
ensGene.txt.gz 2016-11-20 05:59 3.5M
ensPep.sql 2016-11-20 05:59 1.3K
ensPep.txt.gz 2016-11-20 05:59 9.1M
chainHg38.sql 2018-01-07 06:20 1.7K
chainHg38.txt.gz 2018-01-07 06:20 181M
chainHg38Link.sql 2018-01-07 06:21 1.5K
chainHg38Link.txt.gz 2018-01-07 06:22 725M
netHg38.sql 2018-01-07 06:24 2.1K
netHg38.txt.gz 2018-01-07 06:25 36M
ensemblToGeneName.sql 2018-02-04 06:01 1.4K
ensemblToGeneName.txt.gz 2018-02-04 06:01 253K
chromAlias.sql 2018-02-18 05:31 1.4K
chromAlias.txt.gz 2018-02-18 05:31 152K
ucscToRefSeq.sql 2018-02-18 05:31 1.4K
ucscToRefSeq.txt.gz 2018-02-18 05:31 123K
all_mrna.sql 2020-05-05 23:50 2.1K
all_mrna.txt.gz 2020-05-05 23:50 75K
extNcbiRefSeq.sql 2020-05-10 03:26 1.4K
extNcbiRefSeq.txt.gz 2020-05-10 03:26 91
ncbiRefSeq.sql 2020-05-10 03:26 1.9K
ncbiRefSeq.txt.gz 2020-05-10 03:26 3.3M
ncbiRefSeqCds.sql 2020-05-10 03:26 1.3K
ncbiRefSeqCds.txt.gz 2020-05-10 03:26 315K
ncbiRefSeqCurated.sql 2020-05-10 03:26 2.0K
ncbiRefSeqCurated.txt.gz 2020-05-10 03:26 19K
ncbiRefSeqLink.sql 2020-05-10 03:26 2.0K
ncbiRefSeqLink.txt.gz 2020-05-10 03:26 1.7M
ncbiRefSeqOther.sql 2020-05-10 03:26 1.3K
ncbiRefSeqOther.txt.gz 2020-05-10 03:26 75
ncbiRefSeqPepTable.sql 2020-05-10 03:26 1.4K
ncbiRefSeqPepTable.txt.gz 2020-05-10 03:26 9.6M
ncbiRefSeqPredicted.sql 2020-05-10 03:26 2.0K
ncbiRefSeqPredicted.txt.gz 2020-05-10 03:26 3.2M
ncbiRefSeqPsl.sql 2020-05-10 03:26 2.1K
ncbiRefSeqPsl.txt.gz 2020-05-10 03:26 4.2M
seqNcbiRefSeq.sql 2020-05-10 03:26 1.5K
seqNcbiRefSeq.txt.gz 2020-05-10 03:26 879K
xenoMrna.sql 2020-08-18 10:38 2.1K
xenoMrna.txt.gz 2020-08-18 10:38 412M
refGene.sql 2020-08-18 10:48 1.9K
refGene.txt.gz 2020-08-18 10:48 20K
refFlat.sql 2020-08-18 11:00 1.7K
refFlat.txt.gz 2020-08-18 11:00 19K
xenoRefGene.sql 2020-08-18 11:00 2.0K
xenoRefGene.txt.gz 2020-08-18 11:00 36M
xenoRefFlat.sql 2020-08-18 11:03 1.7K
xenoRefFlat.txt.gz 2020-08-18 11:03 32M
mrnaOrientInfo.sql 2020-08-18 11:07 1.8K
mrnaOrientInfo.txt.gz 2020-08-18 11:07 25K
refSeqAli.sql 2020-08-18 11:07 2.1K
refSeqAli.txt.gz 2020-08-18 11:07 22K
xenoRefSeqAli.sql 2020-08-18 11:07 2.1K
xenoRefSeqAli.txt.gz 2020-08-18 11:07 39M
gbLoaded.sql 2020-08-18 11:07 1.6K
gbLoaded.txt.gz 2020-08-18 11:07 113K
trackDb.sql 2024-07-25 09:34 2.1K
trackDb.txt.gz 2024-07-25 09:34 78K
hgFindSpec.sql 2024-07-25 09:34 1.8K
hgFindSpec.txt.gz 2024-07-25 09:34 1.4K
tableDescriptions.sql 2024-11-16 02:03 1.5K
tableDescriptions.txt.gz 2024-11-16 02:03 8.7K
tableList.sql 2024-11-17 03:39 1.6K
tableList.txt.gz 2024-11-17 03:39 5.7K
bigFiles.sql 2024-11-17 03:39 1.4K
bigFiles.txt.gz 2024-11-17 03:39 96