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.

---------------------------------------------------------------
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.

-----------------------------------------------------------------------------
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.
-----------------------------------------------------------------------------
All the files and tables in this directory are freely usable for any purpose.

      Name                        Last modified      Size  Description
Parent Directory - gold.sql 2020-09-02 09:56 1.7K gold.txt.gz 2020-09-02 09:56 21K gap.sql 2020-09-02 09:56 1.6K gap.txt.gz 2020-09-02 09:56 6.3K cpgIslandExtUnmasked.sql 2020-09-02 10:12 1.7K cpgIslandExtUnmasked.txt.gz 2020-09-02 10:12 810K simpleRepeat.sql 2020-09-02 12:20 1.9K simpleRepeat.txt.gz 2020-09-02 12:20 22M gc5BaseBw.sql 2020-09-02 13:12 1.3K gc5BaseBw.txt.gz 2020-09-02 13:12 66 grp.sql 2020-09-02 13:12 1.4K grp.txt.gz 2020-09-02 13:12 213 cytoBandIdeo.sql 2020-09-02 13:52 1.5K cytoBandIdeo.txt.gz 2020-09-02 13:52 6.4K chromInfo.sql 2020-09-02 16:33 1.4K chromInfo.txt.gz 2020-09-02 16:33 6.8K rmsk.sql 2020-09-02 16:36 1.9K rmsk.txt.gz 2020-09-02 16:36 132M nestedRepeats.sql 2020-09-02 16:38 2.0K nestedRepeats.txt.gz 2020-09-02 16:38 16M microsat.sql 2020-09-02 17:30 1.5K microsat.txt.gz 2020-09-02 17:30 447K windowmaskerSdust.sql 2020-09-02 19:26 1.5K windowmaskerSdust.txt.gz 2020-09-02 19:26 138M cpgIslandExt.sql 2020-09-03 10:57 1.7K cpgIslandExt.txt.gz 2020-09-03 10:57 597K chromAlias.sql 2020-09-03 11:38 1.4K chromAlias.txt.gz 2020-09-03 11:38 16K ucscToINSDC.sql 2020-09-04 01:39 1.4K ucscToINSDC.txt.gz 2020-09-04 01:39 8.8K ucscToRefSeq.sql 2020-09-04 01:39 1.5K ucscToRefSeq.txt.gz 2020-09-04 01:39 8.5K chainMm10.sql 2020-09-04 11:25 1.7K chainMm10.txt.gz 2020-09-04 11:25 67M chainMm10Link.sql 2020-09-04 11:29 1.6K chainMm10Link.txt.gz 2020-09-04 11:29 504M netMm10.sql 2020-09-04 11:32 2.1K netMm10.txt.gz 2020-09-04 11:32 68M chainHg38.sql 2020-09-04 11:53 1.7K chainHg38.txt.gz 2020-09-04 11:53 536M chainHg38Link.sql 2020-09-04 12:07 1.6K chainHg38Link.txt.gz 2020-09-04 12:07 1.6G netHg38.sql 2020-09-04 12:10 2.1K netHg38.txt.gz 2020-09-04 12:10 43M augustusGene.sql 2020-09-04 13:18 2.0K augustusGene.txt.gz 2020-09-04 13:18 2.4M chainMm39.sql 2020-09-04 23:44 1.7K chainMm39.txt.gz 2020-09-04 23:44 78M chainMm39Link.sql 2020-09-04 23:48 1.6K chainMm39Link.txt.gz 2020-09-04 23:48 527M netMm39.sql 2020-09-04 23:51 2.1K netMm39.txt.gz 2020-09-04 23:51 68M crisprAllTargets.sql 2020-09-10 14:46 1.3K crisprAllTargets.txt.gz 2020-09-10 14:46 69 genscan.sql 2020-09-17 11:33 1.7K genscan.txt.gz 2020-09-17 11:33 3.0M all_mrna.sql 2020-09-21 09:15 2.1K all_mrna.txt.gz 2020-09-21 09:15 73K xenoMrna.sql 2020-09-21 09:16 2.1K xenoMrna.txt.gz 2020-09-21 09:16 252M refGene.sql 2020-09-21 09:50 1.9K refGene.txt.gz 2020-09-21 09:50 21K refFlat.sql 2020-09-21 09:50 1.7K refFlat.txt.gz 2020-09-21 09:50 19K xenoRefGene.sql 2020-09-21 09:50 2.0K xenoRefGene.txt.gz 2020-09-21 09:50 12M xenoRefFlat.sql 2020-09-21 09:50 1.7K xenoRefFlat.txt.gz 2020-09-21 09:50 11M refSeqAli.sql 2020-09-21 09:50 2.1K refSeqAli.txt.gz 2020-09-21 09:50 22K xenoRefSeqAli.sql 2020-09-21 09:50 2.1K xenoRefSeqAli.txt.gz 2020-09-21 09:50 24M estOrientInfo.sql 2020-09-21 09:52 1.8K estOrientInfo.txt.gz 2020-09-21 09:52 3.0M intronEst.sql 2020-09-21 09:52 2.1K intronEst.txt.gz 2020-09-21 09:52 8.0M all_est.sql 2020-09-21 09:52 2.1K all_est.txt.gz 2020-09-21 09:52 9.6M mrnaOrientInfo.sql 2020-09-21 09:53 1.8K mrnaOrientInfo.txt.gz 2020-09-21 09:53 25K extFile.sql 2020-10-01 14:16 1.4K extFile.txt.gz 2020-10-01 14:16 105 ncbiRefSeq.sql 2020-10-27 12:26 2.0K ncbiRefSeq.txt.gz 2020-10-27 12:26 4.6M ncbiRefSeqCurated.sql 2020-10-27 12:26 2.0K ncbiRefSeqCurated.txt.gz 2020-10-27 12:26 20K ncbiRefSeqPredicted.sql 2020-10-27 12:26 2.0K ncbiRefSeqPredicted.txt.gz 2020-10-27 12:26 4.6M ncbiRefSeqLink.sql 2020-10-27 12:26 2.0K ncbiRefSeqLink.txt.gz 2020-10-27 12:26 2.6M ncbiRefSeqPsl.sql 2020-10-27 12:26 2.1K ncbiRefSeqPsl.txt.gz 2020-10-27 12:26 7.1M ncbiRefSeqOther.sql 2020-10-28 01:39 1.3K ncbiRefSeqOther.txt.gz 2020-10-28 01:39 75 ncbiRefSeqCds.sql 2020-10-28 01:39 1.4K ncbiRefSeqCds.txt.gz 2020-10-28 01:39 594K ncbiRefSeqPepTable.sql 2020-10-28 01:39 1.4K ncbiRefSeqPepTable.txt.gz 2020-10-28 01:39 13M extNcbiRefSeq.sql 2020-10-28 01:39 1.5K extNcbiRefSeq.txt.gz 2020-10-28 01:39 91 seqNcbiRefSeq.sql 2020-10-28 01:39 1.6K seqNcbiRefSeq.txt.gz 2020-10-28 01:39 1.6M chainMacFas5.sql 2020-11-03 00:02 1.7K chainMacFas5.txt.gz 2020-11-03 00:02 432M chainMacFas5Link.sql 2020-11-03 00:15 1.6K chainMacFas5Link.txt.gz 2020-11-03 00:15 1.3G netMacFas5.sql 2020-11-03 00:18 2.1K netMacFas5.txt.gz 2020-11-03 00:18 45M history.sql 2020-11-04 07:48 1.6K history.txt.gz 2020-11-04 07:48 1.4K tableDescriptions.sql 2021-02-13 06:33 1.4K tableDescriptions.txt.gz 2021-02-13 06:33 6.1K trackDb.sql 2021-04-14 15:28 2.1K trackDb.txt.gz 2021-04-14 15:28 37K hgFindSpec.sql 2021-04-14 15:28 1.8K hgFindSpec.txt.gz 2021-04-14 15:28 1.0K bigFiles.sql 2021-04-18 03:03 1.4K bigFiles.txt.gz 2021-04-18 03:03 119 tableList.sql 2021-04-18 03:03 1.6K tableList.txt.gz 2021-04-18 03:03 3.5K