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 - xenoRefSeqAli.txt.gz 2020-08-18 11:07 39M xenoRefSeqAli.sql 2020-08-18 11:07 2.1K xenoRefGene.txt.gz 2020-08-18 11:00 36M xenoRefGene.sql 2020-08-18 11:00 2.0K xenoRefFlat.txt.gz 2020-08-18 11:03 32M xenoRefFlat.sql 2020-08-18 11:03 1.7K xenoMrna.txt.gz 2020-08-18 10:38 412M xenoMrna.sql 2020-08-18 10:38 2.1K ucscToRefSeq.txt.gz 2018-02-18 05:31 123K ucscToRefSeq.sql 2018-02-18 05:31 1.4K ucscToINSDC.txt.gz 2013-09-15 09:31 116K ucscToINSDC.sql 2013-09-15 09:31 1.4K ucscToEnsembl.txt.gz 2014-10-19 08:20 75K ucscToEnsembl.sql 2014-10-19 08:20 1.4K trackDb_pushedout.txt.gz 2023-12-05 13:52 55K trackDb_pushedout.sql 2023-12-05 13:52 2.1K trackDb.txt.gz 2023-12-05 13:52 55K trackDb.sql 2023-12-05 13:52 2.1K tableList.txt.gz 2024-04-14 03:31 5.8K tableList.sql 2024-04-14 03:31 1.6K tableDescriptions.txt.gz 2024-04-13 02:03 8.7K tableDescriptions.sql 2024-04-13 02:03 1.4K tRNAs.txt.gz 2012-04-15 16:35 9.8K tRNAs.sql 2012-04-15 16:35 1.7K simpleRepeat.txt.gz 2010-05-28 14:03 21M simpleRepeat.sql 2010-05-28 14:02 1.9K seqNcbiRefSeq.txt.gz 2020-05-10 03:26 879K seqNcbiRefSeq.sql 2020-05-10 03:26 1.5K rmsk.txt.gz 2010-05-28 13:57 129M rmsk.sql 2010-05-28 13:57 1.8K refSeqAli.txt.gz 2020-08-18 11:07 22K refSeqAli.sql 2020-08-18 11:07 2.1K refGene.txt.gz 2020-08-18 10:48 20K refGene.sql 2020-08-18 10:48 1.9K refFlat.txt.gz 2020-08-18 11:00 19K refFlat.sql 2020-08-18 11:00 1.7K qualityBw.txt.gz 2010-11-07 14:12 61 qualityBw.sql 2010-11-07 14:12 1.2K phyloP13wayAll.txt.gz 2011-10-24 16:18 83M phyloP13wayAll.sql 2011-10-24 16:17 1.7K phastConsElements13way.txt.gz 2011-10-24 16:13 16M phastConsElements13way.sql 2011-10-24 16:13 1.5K phastCons13way.txt.gz 2011-10-24 16:15 73M phastCons13way.sql 2011-10-24 16:14 1.7K nscanPep.txt.gz 2010-05-28 13:58 6.1M nscanPep.sql 2010-05-28 13:58 1.3K nscanGene.txt.gz 2010-05-28 14:14 2.1M nscanGene.sql 2010-05-28 14:14 1.9K netTarSyr2.txt.gz 2015-05-24 21:11 67M netTarSyr2.sql 2015-05-24 21:11 2.1K netRheMac3.txt.gz 2012-12-02 11:12 42M netRheMac3.sql 2012-12-02 11:12 2.1K netPonAbe2.txt.gz 2010-05-28 14:03 40M netPonAbe2.sql 2010-05-28 14:03 2.0K netPapHam1.txt.gz 2012-11-18 11:16 45M netPapHam1.sql 2012-11-18 11:16 2.1K netPanTro3.txt.gz 2011-05-23 07:58 38M netPanTro3.sql 2011-05-23 07:58 2.0K netMonDom5.txt.gz 2010-05-28 13:57 18M netMonDom5.sql 2010-05-28 13:57 2.0K netMm10.txt.gz 2012-05-07 09:01 67M netMm10.sql 2012-05-07 08:59 2.0K netMm9.txt.gz 2010-05-30 13:35 67M netMm9.sql 2010-05-30 13:34 2.0K netMicMur1.txt.gz 2012-11-11 09:31 68M netMicMur1.sql 2012-11-11 09:31 2.1K netHg38.txt.gz 2018-01-07 06:25 36M netHg38.sql 2018-01-07 06:24 2.1K netHg19.txt.gz 2010-05-28 14:09 37M netHg19.sql 2010-05-28 14:08 2.0K netGorGor3.txt.gz 2011-11-27 08:06 38M netGorGor3.sql 2011-11-27 08:06 2.0K netCanFam2.txt.gz 2010-05-28 14:01 73M netCanFam2.sql 2010-05-28 14:00 2.0K nestedRepeats.txt.gz 2010-05-28 14:25 16M nestedRepeats.sql 2010-05-28 14:25 1.9K ncbiRefSeqPsl.txt.gz 2020-05-10 03:26 4.2M ncbiRefSeqPsl.sql 2020-05-10 03:26 2.1K ncbiRefSeqPredicted.txt.gz 2020-05-10 03:26 3.2M ncbiRefSeqPredicted.sql 2020-05-10 03:26 2.0K ncbiRefSeqPepTable.txt.gz 2020-05-10 03:26 9.6M ncbiRefSeqPepTable.sql 2020-05-10 03:26 1.4K ncbiRefSeqOther.txt.gz 2020-05-10 03:26 75 ncbiRefSeqOther.sql 2020-05-10 03:26 1.3K ncbiRefSeqLink.txt.gz 2020-05-10 03:26 1.7M ncbiRefSeqLink.sql 2020-05-10 03:26 2.0K ncbiRefSeqCurated.txt.gz 2020-05-10 03:26 19K ncbiRefSeqCurated.sql 2020-05-10 03:26 2.0K ncbiRefSeqCds.txt.gz 2020-05-10 03:26 315K ncbiRefSeqCds.sql 2020-05-10 03:26 1.3K ncbiRefSeq.txt.gz 2020-05-10 03:26 3.3M ncbiRefSeq.sql 2020-05-10 03:26 1.9K multiz13waySummary.txt.gz 2011-10-24 16:02 28M multiz13waySummary.sql 2011-10-24 16:02 1.5K multiz13wayFrames.txt.gz 2011-10-24 16:04 20M multiz13wayFrames.sql 2011-10-24 16:03 1.7K multiz13way.txt.gz 2011-10-24 16:07 198M multiz13way.sql 2011-10-24 16:05 1.5K mrnaOrientInfo.txt.gz 2020-08-18 11:07 25K mrnaOrientInfo.sql 2020-08-18 11:07 1.8K microsat.txt.gz 2015-08-23 11:23 450K microsat.sql 2015-08-23 11:23 1.5K intronEst.txt.gz 2016-06-12 06:19 8.4M intronEst.sql 2016-06-12 06:19 2.1K history.txt.gz 2010-05-28 14:04 1.0K history.sql 2010-05-28 14:04 1.5K hgFindSpec_pushedout.txt.gz 2023-12-05 13:52 1.4K hgFindSpec_pushedout.sql 2023-12-05 13:52 1.8K hgFindSpec.txt.gz 2023-12-05 13:52 1.4K hgFindSpec.sql 2023-12-05 13:52 1.8K grp.txt.gz 2014-03-02 03:40 208 grp.sql 2014-03-02 03:40 1.3K gold.txt.gz 2010-10-24 13:31 3.4M gold.sql 2010-10-24 13:31 1.6K genscan.txt.gz 2013-12-09 19:32 3.1M genscan.sql 2013-12-09 19:32 1.7K gc5Base.txt.gz 2010-05-28 14:13 12M gc5Base.sql 2010-05-28 14:13 1.7K gbLoaded.txt.gz 2020-08-18 11:07 113K gbLoaded.sql 2020-08-18 11:07 1.6K gap.txt.gz 2010-05-28 14:31 2.5M gap.sql 2010-05-28 14:31 1.5K extNcbiRefSeq.txt.gz 2020-05-10 03:26 91 extNcbiRefSeq.sql 2020-05-10 03:26 1.4K extFile.txt.gz 2011-10-24 16:01 104 extFile.sql 2011-10-24 16:01 1.4K estOrientInfo.txt.gz 2016-06-12 06:19 3.5M estOrientInfo.sql 2016-06-12 06:19 1.8K ensemblToGeneName.txt.gz 2018-02-04 06:01 253K ensemblToGeneName.sql 2018-02-04 06:01 1.4K ensemblSource.txt.gz 2016-11-20 05:54 177K ensemblSource.sql 2016-11-20 05:54 1.4K ensPep.txt.gz 2016-11-20 05:59 9.1M ensPep.sql 2016-11-20 05:59 1.3K ensGtp.txt.gz 2016-11-20 05:58 512K ensGtp.sql 2016-11-20 05:58 1.4K ensGene.txt.gz 2016-11-20 05:59 3.5M ensGene.sql 2016-11-20 05:59 1.9K cytoBandIdeo.txt.gz 2013-04-28 11:15 81K cytoBandIdeo.sql 2013-04-28 11:15 1.5K ctgPos2.txt.gz 2010-05-28 14:03 35K ctgPos2.sql 2010-05-28 14:03 1.5K cpgIslandExtUnmasked.txt.gz 2014-06-01 09:24 788K cpgIslandExtUnmasked.sql 2014-06-01 09:24 1.7K cpgIslandExt.txt.gz 2010-05-28 14:03 720K cpgIslandExt.sql 2010-05-28 14:03 1.6K chromInfo.txt.gz 2010-05-28 14:25 85K chromInfo.sql 2010-05-28 14:25 1.3K chromAlias.txt.gz 2018-02-18 05:31 152K chromAlias.sql 2018-02-18 05:31 1.4K chainTarSyr2Link.txt.gz 2015-05-24 21:07 1.1G chainTarSyr2Link.sql 2015-05-24 21:05 1.5K chainTarSyr2.txt.gz 2015-05-24 21:05 264M chainTarSyr2.sql 2015-05-24 21:04 1.7K chainRheMac3Link.txt.gz 2012-12-02 11:11 219M chainRheMac3Link.sql 2012-12-02 11:11 1.6K chainRheMac3.txt.gz 2012-12-02 11:13 13M chainRheMac3.sql 2012-12-02 11:13 1.7K chainPonAbe2Link.txt.gz 2010-05-28 14:23 249M chainPonAbe2Link.sql 2010-05-28 14:23 1.5K chainPonAbe2.txt.gz 2010-05-28 14:31 17M chainPonAbe2.sql 2010-05-28 14:31 1.6K chainPapHam1Link.txt.gz 2012-11-18 11:16 215M chainPapHam1Link.sql 2012-11-18 11:15 1.6K chainPapHam1.txt.gz 2012-11-18 11:15 17M chainPapHam1.sql 2012-11-18 11:15 1.7K chainPanTro3Link.txt.gz 2011-05-23 08:01 231M chainPanTro3Link.sql 2011-05-23 07:59 1.5K chainPanTro3.txt.gz 2011-05-23 07:59 15M chainPanTro3.sql 2011-05-23 07:59 1.6K chainMonDom5Link.txt.gz 2010-05-28 14:16 741M chainMonDom5Link.sql 2010-05-28 14:14 1.5K chainMonDom5.txt.gz 2010-05-28 14:07 265M chainMonDom5.sql 2010-05-28 14:06 1.6K chainMm10Link.txt.gz 2012-05-07 09:07 484M chainMm10Link.sql 2012-05-07 09:03 1.5K chainMm10.txt.gz 2012-05-07 08:58 64M chainMm10.sql 2012-05-07 08:57 1.6K chainMm9Link.txt.gz 2010-05-28 14:27 460M chainMm9Link.sql 2010-05-28 14:26 1.5K chainMm9.txt.gz 2010-05-28 13:54 57M chainMm9.sql 2010-05-28 13:53 1.6K chainMicMur1Link.txt.gz 2012-11-11 09:29 688M chainMicMur1Link.sql 2012-11-11 09:28 1.6K chainMicMur1.txt.gz 2012-11-11 09:27 209M chainMicMur1.sql 2012-11-11 09:27 1.7K chainHg38Link.txt.gz 2018-01-07 06:22 725M chainHg38Link.sql 2018-01-07 06:21 1.5K chainHg38.txt.gz 2018-01-07 06:20 181M chainHg38.sql 2018-01-07 06:20 1.7K chainHg19Link.txt.gz 2010-05-28 13:59 235M chainHg19Link.sql 2010-05-28 13:58 1.5K chainHg19.txt.gz 2010-05-28 14:00 14M chainHg19.sql 2010-05-28 14:00 1.6K chainGorGor3Link.txt.gz 2011-11-27 08:06 215M chainGorGor3Link.sql 2011-11-27 08:06 1.5K chainGorGor3.txt.gz 2011-11-27 08:05 13M chainGorGor3.sql 2011-11-27 08:05 1.6K chainCanFam2Link.txt.gz 2010-05-28 14:10 490M chainCanFam2Link.sql 2010-05-28 14:09 1.5K chainCanFam2.txt.gz 2010-05-28 14:22 39M chainCanFam2.sql 2010-05-28 14:22 1.6K bigFiles.txt.gz 2024-04-14 03:31 96 bigFiles.sql 2024-04-14 03:31 1.4K bacEnds.txt.gz 2010-10-31 13:39 2.2M bacEnds.sql 2010-10-31 13:39 1.7K bacEndCalJac3Singles.txt.gz 2010-10-31 13:39 907K bacEndCalJac3Singles.sql 2010-10-31 13:39 1.5K augustusGene.txt.gz 2015-07-26 10:54 2.3M augustusGene.sql 2015-07-26 10:54 1.9K all_mrna.txt.gz 2020-05-05 23:50 75K all_mrna.sql 2020-05-05 23:50 2.1K all_est.txt.gz 2016-06-12 06:20 11M all_est.sql 2016-06-12 06:20 2.1K