This directory contains a dump of the UCSC genome annotation database for
the Dec. 2011 (v3.0.1/chrPic1) assembly of the painted turtle genome
(chrPic1, International Painted Turtle Genome Sequencing Consortium (GCA_000241765.1)).
The annotations were generated by UCSC and collaborators worldwide.

For more information about this assembly, please note the NCBI resources:
    http://www.ncbi.nlm.nih.gov/genome/12107
    http://www.ncbi.nlm.nih.gov/genome/assembly/326468
    http://www.ncbi.nlm.nih.gov/bioproject/78657

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=chrPic1
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/chrPic1/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/chrPic1/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/chrPic1/database/gc5BaseBw.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/chrPic1/database/*'
With wget, a single file: 
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/chrPic1/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 chrPic1 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql chrPic1 --local-infile=1 
        -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'

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

---------------------------------------------------------------

      Name                        Last modified      Size  Description
Parent Directory - all_mrna.sql 2020-05-06 04:40 2.1K all_mrna.txt.gz 2020-05-06 04:40 4.3K augustusGene.sql 2015-07-26 11:38 1.9K augustusGene.txt.gz 2015-07-26 11:38 2.2M bigFiles.sql 2021-05-02 03:12 1.4K bigFiles.txt.gz 2021-05-02 03:12 68 chainMm10.sql 2012-06-11 05:59 1.6K chainMm10.txt.gz 2012-06-11 05:59 28M chainMm10Link.sql 2012-06-11 05:05 1.5K chainMm10Link.txt.gz 2012-06-11 05:09 178M chromInfo.sql 2012-06-11 05:23 1.3K chromInfo.txt.gz 2012-06-11 05:23 277K cpgIslandExt.sql 2012-06-08 16:44 1.6K cpgIslandExt.txt.gz 2012-06-08 16:44 663K cpgIslandExtUnmasked.sql 2014-06-01 10:19 1.7K cpgIslandExtUnmasked.txt.gz 2014-06-01 10:19 2.0M cytoBandIdeo.sql 2013-04-28 12:12 1.5K cytoBandIdeo.txt.gz 2013-04-28 12:12 285K gap.sql 2012-06-11 05:23 1.5K gap.txt.gz 2012-06-11 05:23 5.5M gbLoaded.sql 2020-08-18 18:39 1.6K gbLoaded.txt.gz 2020-08-18 18:39 34K gc5BaseBw.sql 2012-06-11 05:41 1.2K gc5BaseBw.txt.gz 2012-06-11 05:41 63 genscan.sql 2012-06-11 05:41 1.6K genscan.txt.gz 2012-06-11 05:41 2.5M genscanSubopt.sql 2012-06-11 05:58 1.5K genscanSubopt.txt.gz 2012-06-11 05:59 5.7M gold.sql 2012-06-11 05:41 1.6K gold.txt.gz 2012-06-11 05:42 7.9M grp.sql 2014-03-02 03:40 1.3K grp.txt.gz 2014-03-02 03:40 208 hgFindSpec.sql 2020-12-06 07:48 1.7K hgFindSpec.txt.gz 2020-12-06 07:48 596 history.sql 2012-06-11 05:26 1.5K history.txt.gz 2012-06-11 05:26 401 microsat.sql 2015-08-23 12:36 1.5K microsat.txt.gz 2015-08-23 12:36 255K mrnaOrientInfo.sql 2020-05-06 04:41 1.8K mrnaOrientInfo.txt.gz 2020-05-06 04:41 1.1K nestedRepeats.sql 2012-06-11 06:01 1.9K nestedRepeats.txt.gz 2012-06-11 06:01 554K netMm10.sql 2012-06-11 06:01 2.0K netMm10.txt.gz 2012-06-11 06:01 11M rmsk.sql 2012-06-11 04:41 1.8K rmsk.txt.gz 2012-06-11 04:42 17M simpleRepeat.sql 2012-06-08 16:43 1.9K simpleRepeat.txt.gz 2012-06-08 16:43 8.9M tableDescriptions.sql 2019-07-21 03:41 1.4K tableDescriptions.txt.gz 2019-07-21 03:41 4.9K tableList.sql 2021-05-02 03:12 1.6K tableList.txt.gz 2021-05-02 03:12 2.0K trackDb.sql 2020-12-06 07:48 2.0K trackDb.txt.gz 2020-12-06 07:48 24K ucscToINSDC.sql 2013-09-15 10:23 1.4K ucscToINSDC.txt.gz 2013-09-15 10:23 480K windowmaskerSdust.sql 2012-06-11 06:02 1.4K windowmaskerSdust.txt.gz 2012-06-11 06:04 107M xenoMrna.sql 2020-08-18 17:59 2.1K xenoMrna.txt.gz 2020-08-18 17:59 296M xenoRefFlat.sql 2020-08-18 18:23 1.7K xenoRefFlat.txt.gz 2020-08-18 18:23 30M xenoRefGene.sql 2020-08-18 18:23 1.9K xenoRefGene.txt.gz 2020-08-18 18:23 34M xenoRefSeqAli.sql 2020-08-18 18:23 2.1K xenoRefSeqAli.txt.gz 2020-08-18 18:23 33M