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 - 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 2021-04-14 15:28 37K 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 2021-02-13 06:33 6.1K tableList.txt.gz 2021-05-09 03:03 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 2021-04-14 15:28 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 2021-04-14 15:28 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 chainMacFas5Link.sql 2020-11-03 00:15 1.6K seqNcbiRefSeq.sql 2020-10-28 01:39 1.6K tableList.sql 2021-05-09 03:03 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 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 tableDescriptions.sql 2021-02-13 06:33 1.4K chromInfo.sql 2020-09-02 16:33 1.4K ncbiRefSeqPepTable.sql 2020-10-28 01:39 1.4K bigFiles.sql 2021-05-09 03:03 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 2021-04-14 15:28 1.0K grp.txt.gz 2020-09-02 13:12 213 bigFiles.txt.gz 2021-05-09 03:03 119 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