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.

---------------------------------------------------------------
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;'

------------------------------------------------------------------
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 2024-06-22 02:03 5.5K tableList.txt.gz 2024-06-23 03:13 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 tableList.sql 2024-06-23 03:13 1.6K genscan.sql 2008-04-23 12:44 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 tableDescriptions.sql 2024-06-22 02:03 1.5K genscanSubopt.sql 2008-04-23 12:44 1.5K phastConsElements9way.sql 2008-04-23 13:04 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 bigFiles.sql 2024-06-23 03:13 1.4K grp.sql 2014-03-02 03:40 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 2024-06-23 03:13 33