This directory contains the May 2011 (gorGor3.1/gorGor3) assembly of the
gorilla genome (gorGor3, Wellcome Trust Sanger Institute May 2011
(NCBI project 31265, GCA_000151905.1)), as well as repeat annotations
and GenBank sequences.

This assembly was produced by the Wellcome Trust Sanger Institute.
For more information on the gorilla genome, see the project website:
	http://www.sanger.ac.uk/resources/downloads/gorilla/
See also, the WGS records:  http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=CABD02

Files included in this directory:

gorGor3.2bit - contains the complete gorilla/gorGor3 genome sequence
    in the 2bit file format.  Repeats from RepeatMasker and Tandem Repeats
    Finder (with period of 12 or less) are shown in lower case; non-repeating
    sequence is shown in upper case.  The utility program, twoBitToFa (available
    from the kent src tree), can be used to extract .fa file(s) from
    this file.  A pre-compiled version of the command line tool can be
    found at:
        http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/
    See also:
        http://genome.ucsc.edu/admin/git.html
	http://genome.ucsc.edu/admin/jk-install.html

gorGor3.agp.gz - Description of how the assembly was generated from
    fragments.

gorGor3.fa.gz - "Soft-masked" assembly sequence in one file.
    Repeats from RepeatMasker and Tandem Repeats Finder (with period
    of 12 or less) are shown in lower case; non-repeating sequence is
    shown in upper case.

gorGor3.fa.masked.gz - "Hard-masked" assembly sequence in one file.
    Repeats are masked by capital Ns; non-repeating sequence is shown in
    upper case.

gorGor3.fa.out.gz - RepeatMasker .out file.  RepeatMasker was run with the
    -s (sensitive) setting.  April 26 2011 (open-3-3-0) version of RepeatMasker
    with RepeatMaskerLib.embl RELEASE 20110920

gorGor3.trf.bed.gz - Tandem Repeats Finder locations, filtered to keep repeats
    with period less than or equal to 12, and translated into UCSC's BED
    format.

md5sum.txt - checksums of files in this directory

mrna.fa.gz - Gorilla mRNA from GenBank. This sequence data is updated
    once a week via automatic GenBank updates.

xenoMrna.fa.gz - GenBank mRNAs from species other than that of 
    the genome. This sequence data is updated once a week via automatic 
    GenBank updates.


gorGor3.chrom.sizes - Two-column tab-separated text file containing assembly
    sequence names and sizes.

gorGor3.gc5Base.wigVarStep.gz - ascii data wiggle variable step values used
                           - to construct the GC Percent track
gorGor3.gc5Base.wig.gz - wiggle database table for the GC Percent track
                    - this is an older standard alternative to the current
                    - bigWig format of the track, sometimes usefull for analysis
gorGor3.gc5Base.wib    - binary data to correspond with the gc5Base.wig file
    see also:  http://genome.ucsc.edu/goldenPath/help/wiggle.html
    and  http://genomewiki.ucsc.edu/index.php/Using_hgWiggle_without_a_database
         for a discussion of how to use the wig.gz and .wib files for
         interaction with the GC percent data values

gorGor3.chromAlias.txt - sequence name alias file, one line
    for each sequence name.  First column is sequence name followed by
    tab separated alias names.

------------------------------------------------------------------
If you plan to download a large file or multiple files from this
directory, we recommend that you use ftp rather than downloading the
files via our website. To do so, ftp to hgdownload.cse.ucsc.edu
[username: anonymous, password: your email address], then cd to the
directory goldenPath/gorGor3/bigZips. 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/gorGor3/bigZips/ .
For a single file, e.g. chromFa.tar.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/gorGor3/bigZips/chromFa.tar.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/gorGor3/bigZips/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/gorGor3/bigZips/chromFa.tar.gz' 
        -O chromFa.tar.gz

To unpack the *.tar.gz files:
    tar xvzf <file>.tar.gz
To uncompress the fa.gz files:
    gunzip <file>.fa.gz

------------------------------------------------------------------
Please note the following data sharing guidelines:

http://www.sanger.ac.uk/datasharing/
      Name                          Last modified      Size  Description
Parent Directory - xenoRefMrna.fa.gz.md5 2020-02-28 04:06 52 xenoRefMrna.fa.gz 2020-02-28 04:06 336M xenoMrna.fa.gz.md5 2020-02-28 04:06 49 xenoMrna.fa.gz 2020-02-28 04:05 6.8G upstream5000.fa.gz.md5 2020-02-28 04:08 53 upstream5000.fa.gz 2020-02-28 04:08 16M upstream2000.fa.gz.md5 2020-02-28 04:07 53 upstream2000.fa.gz 2020-02-28 04:07 6.7M upstream1000.fa.gz.md5 2020-02-28 04:07 53 upstream1000.fa.gz 2020-02-28 04:07 3.5M mrna.fa.gz.md5 2020-02-28 03:55 45 mrna.fa.gz 2020-02-28 03:55 108K md5sum.txt 2019-01-17 15:54 479 gorGor3.trf.bed.gz 2011-11-14 10:45 6.0M gorGor3.gc5Base.wigVarStep.gz 2011-10-11 15:47 1.4G gorGor3.gc5Base.wig.gz 2019-01-17 14:49 13M gorGor3.gc5Base.wib 2019-01-17 14:49 559M gorGor3.fa.out.gz 2011-11-14 10:45 158M gorGor3.fa.masked.gz 2011-11-14 11:06 468M gorGor3.fa.gz 2011-11-14 10:59 867M gorGor3.chromAlias.txt 2020-09-29 10:48 256 gorGor3.chrom.sizes 2011-10-11 14:51 800K gorGor3.agp.gz 2011-11-14 10:44 739K gorGor3.2bit 2011-10-14 15:13 758M genes/ 2020-02-05 13:47 -