This directory contains a dump of the UCSC genome annotation database for
the Feb. 2009 assembly of the human genome (hg19, GRCh37 Genome Reference
Consortium Human Reference 37 (GCA_000001405.1)).

The annotations were generated by UCSC and collaborators worldwide.

The Feb. 2009 human reference sequence (GRCh37) was produced by the
Genome Reference Consortium:

Note on chrM:
Since the release of the UCSC hg19 assembly, the Homo sapiens mitochondrion
sequence (represented as "chrM" in the Genome Browser) has been replaced in
GenBank with the record NC_012920. We have not replaced the original sequence,
NC_001807, in the hg19 Genome Browser. We plan to use the Revised Cambridge
Reference Sequence (rCRS,
in the next human assembly release.

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:
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, then go to 
the directory goldenPath/hg19/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:// .
For a single file, e.g. gc5BaseBw.txt.gz
    rsync -avzP 
        rsync:// .

Or with wget, all files:
    wget --timestamping 
With wget, a single file: 
    wget --timestamping 
        -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

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 hg19 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql hg19 --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.
[ICO]NameLast modifiedSizeDescription

[DIR]Parent Directory  -  
[TXT]README.txt20-Jan-2017 13:22 3.2K 
[TXT]README.txte19-Sep-2012 12:19 3.0K 
[   ]snp134_preview.sql02-Sep-2011 14:00 3.2K 
[   ]snp134_preview.txt.gz02-Sep-2011 14:03 1.0G 
[   ]snp135_preview.sql15-Nov-2011 10:57 3.2K 
[   ]snp135_preview.txt.gz15-Nov-2011 11:02 1.2G 
[   ]snp137_preview.sql26-Nov-2012 12:10 3.2K 
[   ]snp137_preview.txt.gz26-Nov-2012 12:14 1.4G 
[   ]snp141_preview.sql20-Oct-2014 13:27 3.2K 
[   ]snp141_preview.txt.gz20-Oct-2014 13:33 1.6G 

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