This directory contains a dump of the UCSC genome annotation database for the
May 2020 (Callithrix_jacchus_cj1700_1.1/calJac4) assembly of the marmoset genome
(calJac4, McDonnell Genome Institute at Washington University) .
The annotations were generated by UCSC and collaborators worldwide.
For more information about this assembly, please note the NCBI resources:
https://www.ncbi.nlm.nih.gov/genome/442
https://www.ncbi.nlm.nih.gov/genome/assembly/7157801
https://www.ncbi.nlm.nih.gov/bioproject/566173
https://www.ncbi.nlm.nih.gov/biosample/SAMN12783337
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=calJac4
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.soe.ucsc.edu, then go to
the directory goldenPath/calJac4/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.soe.ucsc.edu/goldenPath/calJac4/database/ .
For a single file, e.g. gc5Base.txt.gz
rsync -avzP
rsync://hgdownload.soe.ucsc.edu/goldenPath/calJac4/database/gc5Base.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.soe.ucsc.edu/goldenPath/calJac4/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.soe.ucsc.edu/goldenPath/calJac4/database/gc5Base.txt.gz'
-O gc5Base.txt.gz
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 calJac4 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql calJac4 --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.
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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 -
chainHg38Link.txt.gz 2020-09-04 12:07 1.6G
chainMacFas5Link.txt.gz 2020-11-03 00:15 1.3G
chainHg38.txt.gz 2020-09-04 11:53 536M
chainMm39Link.txt.gz 2020-09-04 23:48 527M
chainMm10Link.txt.gz 2020-09-04 11:29 504M
chainMacFas5.txt.gz 2020-11-03 00:02 432M
xenoMrna.txt.gz 2020-09-21 09:16 252M
windowmaskerSdust.txt.gz 2020-09-02 19:26 138M
rmsk.txt.gz 2020-09-02 16:36 132M
chainMm39.txt.gz 2020-09-04 23:44 78M
netMm39.txt.gz 2020-09-04 23:51 68M
netMm10.txt.gz 2020-09-04 11:32 68M
chainMm10.txt.gz 2020-09-04 11:25 67M
netMacFas5.txt.gz 2020-11-03 00:18 45M
netHg38.txt.gz 2020-09-04 12:10 43M
xenoRefSeqAli.txt.gz 2020-09-21 09:50 24M
simpleRepeat.txt.gz 2020-09-02 12:20 22M
nestedRepeats.txt.gz 2020-09-02 16:38 16M
ncbiRefSeqPepTable.txt.gz 2020-10-28 01:39 13M
xenoRefGene.txt.gz 2020-09-21 09:50 12M
xenoRefFlat.txt.gz 2020-09-21 09:50 11M
all_est.txt.gz 2020-09-21 09:52 9.6M
intronEst.txt.gz 2020-09-21 09:52 8.0M
ncbiRefSeqPsl.txt.gz 2020-10-27 12:26 7.1M
ncbiRefSeq.txt.gz 2020-10-27 12:26 4.6M
ncbiRefSeqPredicted.txt.gz 2020-10-27 12:26 4.6M
estOrientInfo.txt.gz 2020-09-21 09:52 3.0M
genscan.txt.gz 2020-09-17 11:33 3.0M
ncbiRefSeqLink.txt.gz 2020-10-27 12:26 2.6M
augustusGene.txt.gz 2020-09-04 13:18 2.4M
seqNcbiRefSeq.txt.gz 2020-10-28 01:39 1.6M
cpgIslandExtUnmasked.txt.gz 2020-09-02 10:12 810K
cpgIslandExt.txt.gz 2020-09-03 10:57 597K
ncbiRefSeqCds.txt.gz 2020-10-28 01:39 594K
microsat.txt.gz 2020-09-02 17:30 447K
all_mrna.txt.gz 2020-09-21 09:15 73K
trackDb.txt.gz 2023-12-05 13:52 32K
mrnaOrientInfo.txt.gz 2020-09-21 09:53 25K
refSeqAli.txt.gz 2020-09-21 09:50 22K
gold.txt.gz 2020-09-02 09:56 21K
refGene.txt.gz 2020-09-21 09:50 21K
ncbiRefSeqCurated.txt.gz 2020-10-27 12:26 20K
refFlat.txt.gz 2020-09-21 09:50 19K
chromAlias.txt.gz 2020-09-03 11:38 16K
ucscToINSDC.txt.gz 2020-09-04 01:39 8.8K
ucscToRefSeq.txt.gz 2020-09-04 01:39 8.5K
chromInfo.txt.gz 2020-09-02 16:33 6.8K
cytoBandIdeo.txt.gz 2020-09-02 13:52 6.4K
gap.txt.gz 2020-09-02 09:56 6.3K
tableDescriptions.txt.gz 2024-11-16 02:04 6.1K
tableList.txt.gz 2024-11-17 03:13 3.5K
xenoRefSeqAli.sql 2020-09-21 09:50 2.1K
ncbiRefSeqPsl.sql 2020-10-27 12:26 2.1K
refSeqAli.sql 2020-09-21 09:50 2.1K
intronEst.sql 2020-09-21 09:52 2.1K
xenoMrna.sql 2020-09-21 09:16 2.1K
all_mrna.sql 2020-09-21 09:15 2.1K
all_est.sql 2020-09-21 09:52 2.1K
netMacFas5.sql 2020-11-03 00:18 2.1K
netMm39.sql 2020-09-04 23:51 2.1K
netMm10.sql 2020-09-04 11:32 2.1K
netHg38.sql 2020-09-04 12:10 2.1K
trackDb.sql 2023-12-05 13:52 2.1K
ncbiRefSeqLink.sql 2020-10-27 12:26 2.0K
ncbiRefSeqPredicted.sql 2020-10-27 12:26 2.0K
ncbiRefSeqCurated.sql 2020-10-27 12:26 2.0K
augustusGene.sql 2020-09-04 13:18 2.0K
xenoRefGene.sql 2020-09-21 09:50 2.0K
nestedRepeats.sql 2020-09-02 16:38 2.0K
ncbiRefSeq.sql 2020-10-27 12:26 2.0K
simpleRepeat.sql 2020-09-02 12:20 1.9K
refGene.sql 2020-09-21 09:50 1.9K
rmsk.sql 2020-09-02 16:36 1.9K
mrnaOrientInfo.sql 2020-09-21 09:53 1.8K
estOrientInfo.sql 2020-09-21 09:52 1.8K
hgFindSpec.sql 2023-12-05 13:52 1.8K
xenoRefFlat.sql 2020-09-21 09:50 1.7K
cpgIslandExtUnmasked.sql 2020-09-02 10:12 1.7K
chainMacFas5.sql 2020-11-03 00:02 1.7K
refFlat.sql 2020-09-21 09:50 1.7K
chainMm39.sql 2020-09-04 23:44 1.7K
chainMm10.sql 2020-09-04 11:25 1.7K
chainHg38.sql 2020-09-04 11:53 1.7K
cpgIslandExt.sql 2020-09-03 10:57 1.7K
genscan.sql 2020-09-17 11:33 1.7K
gold.sql 2020-09-02 09:56 1.7K
gap.sql 2020-09-02 09:56 1.6K
history.sql 2020-11-04 07:48 1.6K
tableList.sql 2024-11-17 03:13 1.6K
chainMacFas5Link.sql 2020-11-03 00:15 1.6K
seqNcbiRefSeq.sql 2020-10-28 01:39 1.6K
chainMm39Link.sql 2020-09-04 23:48 1.6K
chainMm10Link.sql 2020-09-04 11:29 1.6K
chainHg38Link.sql 2020-09-04 12:07 1.6K
cytoBandIdeo.sql 2020-09-02 13:52 1.5K
windowmaskerSdust.sql 2020-09-02 19:26 1.5K
microsat.sql 2020-09-02 17:30 1.5K
extNcbiRefSeq.sql 2020-10-28 01:39 1.5K
tableDescriptions.sql 2024-11-16 02:04 1.5K
ucscToRefSeq.sql 2020-09-04 01:39 1.5K
ucscToINSDC.sql 2020-09-04 01:39 1.4K
chromAlias.sql 2020-09-03 11:38 1.4K
extFile.sql 2020-10-01 14:16 1.4K
chromInfo.sql 2020-09-02 16:33 1.4K
bigFiles.sql 2024-11-17 03:13 1.4K
ncbiRefSeqPepTable.sql 2020-10-28 01:39 1.4K
grp.sql 2020-09-02 13:12 1.4K
ncbiRefSeqCds.sql 2020-10-28 01:39 1.4K
history.txt.gz 2020-11-04 07:48 1.4K
crisprAllTargets.sql 2020-09-10 14:46 1.3K
ncbiRefSeqOther.sql 2020-10-28 01:39 1.3K
gc5BaseBw.sql 2020-09-02 13:12 1.3K
hgFindSpec.txt.gz 2023-12-05 13:52 1.1K
grp.txt.gz 2020-09-02 13:12 213
bigFiles.txt.gz 2024-11-17 03:13 119
extFile.txt.gz 2020-10-01 14:16 105
extNcbiRefSeq.txt.gz 2020-10-28 01:39 91
ncbiRefSeqOther.txt.gz 2020-10-28 01:39 75
crisprAllTargets.txt.gz 2020-09-10 14:46 69
gc5BaseBw.txt.gz 2020-09-02 13:12 66