This directory contains the Jul. 2011 (HetGla_1.0/hetGla1) assembly of the naked mole-rat genome
(hetGla1, HetGla_1.0 (NCBI project 68323, accession GCA_000230455.1)), as well as repeat annotations and GenBank sequences.

This assembly was produced by the National Center for Biotechnology Information (NCBI).
For more information on the naked mole-rat genome, see the project website:
http://www.ncbi.nlm.nih.gov/bioproject/68323

Files included in this directory:

hetGla1.2bit - contains the complete naked mole-rat/hetGla1 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

hetGla1.agp.gz - Description of how the assembly was generated from
    fragments.

hetGla1.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.

hetGla1.fa.masked.gz - "Hard-masked" assembly sequence in one file.
    Repeats are masked by capital Ns; non-repeating sequence is shown in
    upper case.

hetGla1.fa.out.gz - RepeatMasker .out file.  RepeatMasker was run with the
    -s (sensitive) setting. RepeatMasker version: April 26 2011 (open-3-3-0) (open-3-2-9)
    RepeatMasker library version: 0110920 

hetGla1.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 - Naked mole-rat 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.

hetGla1.chrom.sizes - Two-column tab-separated text file containing assembly
    sequence names and sizes.

hetGla1.gc5Base.wigVarStep.gz - ascii data wiggle variable step values used
                           - to construct the GC Percent track
hetGla1.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
hetGla1.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

hetGla1.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/hetGla1/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/hetGla1/bigZips/ .
For a single file, e.g. chromFa.tar.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/hetGla1/bigZips/chromFa.tar.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/hetGla1/bigZips/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/hetGla1/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 06:18 20 est.fa.gz.md5 2019-10-17 06:18 44 genes/ 2020-10-02 13:37 - hetGla1.2bit 2011-12-07 09:53 742M hetGla1.agp.gz 2012-01-04 14:06 6.3M hetGla1.chrom.sizes 2011-12-02 15:40 515K hetGla1.chromAlias.txt 2020-09-29 10:48 767K hetGla1.fa.gz 2012-01-04 14:19 781M hetGla1.fa.masked.gz 2012-01-04 14:29 564M hetGla1.fa.out.gz 2012-01-04 14:07 126M hetGla1.gc5Base.wib 2019-01-17 14:49 480M hetGla1.gc5Base.wig.gz 2019-01-17 14:49 11M hetGla1.gc5Base.wigVarStep.gz 2011-12-02 15:46 1.2G hetGla1.trf.bed.gz 2012-01-04 14:07 4.3M md5sum.txt 2019-01-17 15:54 479 mrna.fa.gz 2019-10-17 06:04 136K mrna.fa.gz.md5 2019-10-17 06:04 45 xenoMrna.fa.gz 2019-10-17 06:14 6.8G xenoMrna.fa.gz.md5 2019-10-17 06:14 49 xenoRefMrna.fa.gz 2019-10-17 06:18 331M xenoRefMrna.fa.gz.md5 2019-10-17 06:18 52