This directory contains the Dec. 2009 (TGC Turkey_2.01/melGal1) assembly of the turkey genome
(melGal1, TGC (NCBI Project ID: 10805, Accession: GCA_000146605.1)), as well as repeat annotations and GenBank sequences.

This assembly was produced by the Turkey Genome Consortium.
For more information on the turkey genome, see the project website:
http://www.vtnews.vt.edu/articles/2010/09/090810-cals-genome.html 
http://www.ncbi.nlm.nih.gov/bioproject/10805

Files included in this directory:

melGal1.2bit - contains the complete turkey/melGal1 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

melGal1.agp.gz - Description of how the assembly was generated from
    fragments.

melGal1.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.

melGal1.fa.masked.gz - "Hard-masked" assembly sequence in one file.
    Repeats are masked by capital Ns; non-repeating sequence is shown in
    upper case.

melGal1.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
  
melGal1.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.

est.fa.gz - Turkey ESTs in GenBank. This sequence data is updated once a
    week via automatic GenBank updates.

md5sum.txt - checksums of files in this directory

mrna.fa.gz - Turkey 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.

melGal1.chrom.sizes - Two-column tab-separated text file containing assembly
    sequence names and sizes.

melGal1.gc5Base.wigVarStep.gz - ascii data wiggle variable step values used
                           - to construct the GC Percent track
melGal1.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
melGal1.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

melGal1.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/melGal1/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/melGal1/bigZips/ .
For a single file, e.g. chromFa.tar.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/melGal1/bigZips/chromFa.tar.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/melGal1/bigZips/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/melGal1/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


      Name                          Last modified      Size  Description
Parent Directory - est.fa.gz 2019-10-17 11:41 4.0M est.fa.gz.md5 2019-10-17 11:41 44 genes/ 2020-10-02 13:38 - md5sum.txt 2019-01-17 15:55 479 melGal1.2bit 2010-11-05 12:16 257M melGal1.agp.gz 2011-03-08 19:40 3.9M melGal1.chrom.sizes 2010-11-04 12:07 115K melGal1.chromAlias.txt 2020-09-29 10:49 236K melGal1.fa.gz 2011-03-08 19:44 290M melGal1.fa.masked.gz 2011-03-08 19:49 267M melGal1.fa.out.gz 2011-03-08 19:40 10M melGal1.gc5Base.wib 2019-01-17 14:48 185M melGal1.gc5Base.wig.gz 2019-01-17 14:48 4.2M melGal1.gc5Base.wigVarStep.gz 2010-11-04 12:09 477M melGal1.trf.bed.gz 2011-03-08 19:40 1.0M mrna.fa.gz 2019-10-17 11:25 117K mrna.fa.gz.md5 2019-10-17 11:25 45 upstream1000.fa.gz 2019-10-17 11:41 640K upstream1000.fa.gz.md5 2019-10-17 11:41 53 upstream2000.fa.gz 2019-10-17 11:41 1.2M upstream2000.fa.gz.md5 2019-10-17 11:41 53 upstream5000.fa.gz 2019-10-17 11:41 2.9M upstream5000.fa.gz.md5 2019-10-17 11:41 53 xenoMrna.fa.gz 2019-10-17 11:36 6.8G xenoMrna.fa.gz.md5 2019-10-17 11:36 49 xenoRefMrna.fa.gz 2019-10-17 11:41 331M xenoRefMrna.fa.gz.md5 2019-10-17 11:41 52