This directory contains a dump of the UCSC genome annotation database for
the Mar. 2012 (RGSC 5.0/rn5) assembly of the rat genome
(rn5, RGSC Rnor_5.0 (GCA_000001895.3)) from the
Rat Genome Sequencing Consortium.  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/73
    http://www.ncbi.nlm.nih.gov/genome/assembly/382928
    http://www.ncbi.nlm.nih.gov/bioproject/16219

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=rn5
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/rn5/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/rn5/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/rn5/database/gc5BaseBw.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/rn5/database/*'
With wget, a single file: 
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/rn5/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 rn5 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql rn5 --local-infile=1 
        -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'

------------------------------------------------------------------
These data are  made available before scientific publication 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
   particular genes and regions if the providers of this data (the Rat
   Genome Sequencing Consortium) are properly acknowledged.
3. The Centers producing the data reserve the right to publish the
   initial large-scale analyses of the dataset, 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. This is in accordance with, and with the understandings in the Fort
   Lauderdale meeting discussing Community Resource Projects (see
   http://www.wellcome.ac.uk/en/1/awtpubrepdat.html) and the resulting
   NHGRI policy statement
   (http://www.genome.gov/page.cfm?pageID=10506537).
5. Any redistribution of the data should carry this notice.
      Name                          Last modified      Size  Description
Parent Directory - all_est.sql 2016-05-15 11:25 2.1K all_est.txt.gz 2016-05-15 11:25 46M all_mrna.sql 2020-08-20 08:23 2.1K all_mrna.txt.gz 2020-08-20 08:23 4.1M augustusGene.sql 2015-07-26 17:21 1.9K augustusGene.txt.gz 2015-07-26 17:21 2.4M bigFiles.sql 2021-05-02 03:12 1.4K bigFiles.txt.gz 2021-05-02 03:12 86 chainMm10.sql 2012-06-17 21:29 1.6K chainMm10.txt.gz 2012-06-17 21:30 179M chainMm10Link.sql 2012-06-17 20:52 1.5K chainMm10Link.txt.gz 2012-06-17 20:59 1.0G chainPanTro4.sql 2014-01-26 18:29 1.7K chainPanTro4.txt.gz 2014-01-26 18:29 56M chainPanTro4Link.sql 2014-01-26 18:29 1.5K chainPanTro4Link.txt.gz 2014-01-26 18:30 485M chainRheMac3.sql 2012-12-02 21:09 1.7K chainRheMac3.txt.gz 2012-12-02 21:09 51M chainRheMac3Link.sql 2012-12-02 21:07 1.5K chainRheMac3Link.txt.gz 2012-12-02 21:07 444M chromAlias.sql 2016-09-15 18:03 1.4K chromAlias.txt.gz 2016-09-15 18:03 1.1K chromInfo.sql 2012-06-17 21:36 1.3K chromInfo.txt.gz 2012-06-17 21:36 16K cpgIslandExt.sql 2012-06-17 21:34 1.6K cpgIslandExt.txt.gz 2012-06-17 21:34 378K cpgIslandExtUnmasked.sql 2014-06-01 19:35 1.7K cpgIslandExtUnmasked.txt.gz 2014-06-01 19:35 447K crisprRanges.sql 2016-11-06 09:26 1.4K crisprRanges.txt.gz 2016-11-06 09:26 1.3M crisprTargets.sql 2016-11-06 09:26 1.3K crisprTargets.txt.gz 2016-11-06 09:26 59 cytoBand.sql 2013-07-28 06:10 1.5K cytoBand.txt.gz 2013-07-28 06:10 2.3K cytoBandIdeo.sql 2013-07-28 06:10 1.5K cytoBandIdeo.txt.gz 2013-07-28 06:10 17K ensGene.sql 2015-02-09 04:18 1.9K ensGene.txt.gz 2015-02-09 04:18 2.4M ensGtp.sql 2015-02-09 04:17 1.4K ensGtp.txt.gz 2015-02-09 04:17 308K ensPep.sql 2015-02-09 04:16 1.3K ensPep.txt.gz 2015-02-09 04:16 7.5M ensemblSource.sql 2015-02-09 04:17 1.3K ensemblSource.txt.gz 2015-02-09 04:17 89K ensemblToGeneName.sql 2015-02-09 04:17 1.4K ensemblToGeneName.txt.gz 2015-02-09 04:17 230K estOrientInfo.sql 2016-05-15 11:26 1.8K estOrientInfo.txt.gz 2016-05-15 11:26 13M extFile.sql 2014-06-22 17:01 1.4K extFile.txt.gz 2014-06-22 17:01 77 gap.sql 2012-06-17 21:32 1.5K gap.txt.gz 2012-06-17 21:32 2.9M gbLoaded.sql 2020-08-20 08:47 1.6K gbLoaded.txt.gz 2020-08-20 08:47 44K gc5BaseBw.sql 2012-06-17 21:28 1.2K gc5BaseBw.txt.gz 2012-06-17 21:28 59 genscan.sql 2012-06-17 21:29 1.6K genscan.txt.gz 2012-06-17 21:29 3.1M genscanSubopt.sql 2012-06-11 07:53 1.5K genscanSubopt.txt.gz 2012-06-11 07:54 6.6M gold.sql 2012-06-17 21:33 1.6K gold.txt.gz 2012-06-17 21:33 2.0M grp.sql 2014-03-02 04:14 1.3K grp.txt.gz 2014-03-02 04:14 208 hgFindSpec.sql 2020-10-25 08:25 1.7K hgFindSpec.txt.gz 2020-10-25 08:25 935 history.sql 2012-06-17 21:29 1.5K history.txt.gz 2012-06-17 21:29 391 intronEst.sql 2016-05-15 11:27 2.1K intronEst.txt.gz 2016-05-15 11:27 24M locusName.sql 2016-11-06 09:26 1.5K locusName.txt.gz 2016-11-06 09:26 3.4M mgcFullMrna.sql 2020-03-01 08:51 2.1K mgcFullMrna.txt.gz 2020-03-01 08:51 666K mgcGenes.sql 2020-03-01 08:52 1.9K mgcGenes.txt.gz 2020-03-01 08:52 614K microsat.sql 2015-08-24 01:15 1.5K microsat.txt.gz 2015-08-24 01:15 2.2M mrnaOrientInfo.sql 2020-08-20 08:47 1.8K mrnaOrientInfo.txt.gz 2020-08-20 08:47 1.7M multiz13way.sql 2014-06-22 17:01 1.5K multiz13way.txt.gz 2014-06-22 17:01 207M multiz13wayFrames.sql 2014-06-22 17:02 1.7K multiz13wayFrames.txt.gz 2014-06-22 17:02 23M multiz13waySummary.sql 2014-06-22 17:02 1.6K multiz13waySummary.txt.gz 2014-06-22 17:02 30M nestedRepeats.sql 2012-06-17 21:33 1.9K nestedRepeats.txt.gz 2012-06-17 21:33 11M netMm10.sql 2012-06-17 20:47 2.0K netMm10.txt.gz 2012-06-17 20:48 56M netPanTro4.sql 2014-01-26 18:32 2.1K netPanTro4.txt.gz 2014-01-26 18:32 51M netRheMac3.sql 2012-12-02 21:09 2.1K netRheMac3.txt.gz 2012-12-02 21:09 51M phastCons13way.sql 2014-06-22 17:02 1.8K phastCons13way.txt.gz 2014-06-22 17:02 65M phastConsElements13way.sql 2014-06-22 17:02 1.6K phastConsElements13way.txt.gz 2014-06-22 17:02 16M phyloP13way.sql 2014-06-22 17:03 1.8K phyloP13way.txt.gz 2014-06-22 17:03 72M refFlat.sql 2020-08-20 08:47 1.7K refFlat.txt.gz 2020-08-20 08:47 1.7M refGene.sql 2020-08-20 08:47 1.9K refGene.txt.gz 2020-08-20 08:47 1.9M refSeqAli.sql 2020-08-20 08:47 2.1K refSeqAli.txt.gz 2020-08-20 08:47 1.8M rmsk.sql 2012-06-17 21:29 1.8K rmsk.txt.gz 2012-06-17 21:30 123M simpleRepeat.sql 2012-06-17 21:37 1.9K simpleRepeat.txt.gz 2012-06-17 21:37 36M tableDescriptions.sql 2020-10-10 02:03 1.4K tableDescriptions.txt.gz 2020-10-10 02:03 6.7K tableList.sql 2021-05-02 03:12 1.6K tableList.txt.gz 2021-05-02 03:12 3.6K trackDb.sql 2020-10-24 07:08 2.0K trackDb.txt.gz 2020-10-24 07:08 43K ucscToINSDC.sql 2013-09-15 19:12 1.4K ucscToINSDC.txt.gz 2013-09-15 19:12 22K windowmaskerSdust.sql 2012-06-17 20:45 1.4K windowmaskerSdust.txt.gz 2012-06-17 20:43 127M xenoMrna.sql 2020-08-20 08:23 2.1K xenoMrna.txt.gz 2020-08-20 08:23 236M xenoRefFlat.sql 2020-08-20 08:47 1.7K xenoRefFlat.txt.gz 2020-08-20 08:47 22M xenoRefGene.sql 2020-08-20 08:47 1.9K xenoRefGene.txt.gz 2020-08-20 08:47 24M xenoRefSeqAli.sql 2020-08-20 08:47 2.1K xenoRefSeqAli.txt.gz 2020-08-20 08:47 24M