This directory contains the Oct. 2010 (CGSC 2.1.3/panTro3) assembly of
the chimp genome (panTro3, CGSC 2.1.3 (GCA_000001515.3)), as well as
repeat annotations and GenBank sequences.

This assembly was produced by Chimpanzee Sequencing and Analysis Consortium.

For more information on the chimp genome, see the project website:
http://genome.wustl.edu/genomes/view/pan_troglodytes/

Files included in this directory:

panTro3.2bit - contains the complete chimp/panTro3 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

panTro3.agp.gz - Description of how the assembly was generated from
    fragments.

panTro3.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.

panTro3.fa.masked.gz - "Hard-masked" assembly sequence in one file.
    Repeats are masked by capital Ns; non-repeating sequence is shown in
    upper case.

panTro3.fa.out.gz - RepeatMasker .out file.  RepeatMasker was run with the
    -s (sensitive) setting.  RepeatMasker version: June 30 2010 (open-3-2-9)
    RepeatMasker library version: 20090604

panTro3.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

upstream1000.fa.gz - Sequences 1000 bases upstream of annotated
transcription starts of RefSeq genes with annotated 5' UTRs.
This file is updated weekly so it might be slightly out of sync with
the RefSeq data which is updated daily for most assemblies.

upstream2000.fa.gz - Same as upstream1000, but 2000 bases.

upstream5000.fa.gz - Same as upstream1000, but 5000 bases.

panTro3.chrom.sizes - Two-column tab-separated text file containing assembly
    sequence names and sizes.

panTro3.gc5Base.wigVarStep.gz - ascii data wiggle variable step values used
                           - to construct the GC Percent track
panTro3.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
panTro3.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

panTro3.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/panTro3/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/panTro3/bigZips/ .
For a single file, e.g. chromFa.tar.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/panTro3/bigZips/chromFa.tar.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/panTro3/bigZips/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/panTro3/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

The chimpanzee sequence is made freely 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 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.
      Name                          Last modified      Size  Description
Parent Directory - est.fa.gz 2019-10-17 16:29 2.7M est.fa.gz.md5 2019-10-17 16:29 44 genes/ 2020-02-05 13:47 - md5sum.txt 2019-01-17 15:57 479 mrna.fa.gz 2019-10-17 16:14 1.9M mrna.fa.gz.md5 2019-10-17 16:14 45 panTro3.2bit 2011-02-22 09:30 822M panTro3.agp.gz 2011-02-23 13:11 4.4M panTro3.chrom.sizes 2011-02-17 14:20 654K panTro3.chromAlias.txt 2020-09-29 10:49 887K panTro3.fa.gz 2011-02-23 13:27 905M panTro3.fa.masked.gz 2011-02-23 13:36 479M panTro3.fa.out.gz 2011-02-23 13:13 163M panTro3.gc5Base.wib 2019-01-17 14:52 566M panTro3.gc5Base.wig.gz 2019-01-17 14:52 12M panTro3.gc5Base.wigVarStep.gz 2011-02-17 14:29 1.4G panTro3.trf.bed.gz 2011-02-23 13:13 7.3M refMrna.fa.gz 2019-10-17 16:29 1.5M refMrna.fa.gz.md5 2019-10-17 16:29 48 upstream1000.fa.gz 2019-10-17 16:30 3.9M upstream1000.fa.gz.md5 2019-10-17 16:30 53 upstream2000.fa.gz 2019-10-17 16:31 7.4M upstream2000.fa.gz.md5 2019-10-17 16:31 53 upstream5000.fa.gz 2019-10-17 16:31 18M upstream5000.fa.gz.md5 2019-10-17 16:31 53 xenoMrna.fa.gz 2019-10-17 16:25 6.8G xenoMrna.fa.gz.md5 2019-10-17 16:25 49 xenoRefMrna.fa.gz 2019-10-17 16:29 329M xenoRefMrna.fa.gz.md5 2019-10-17 16:29 52