This directory contains the Jun. 2020 (GRCm39/mm39) assembly of the
    mouse genome (mm39, Genome Reference Consortium Mouse Build 39 (GCA_000001635.9)),
    as well as repeat annotations and GenBank sequences.

For more information about this assembly, please note the NCBI resources:
    https://www.ncbi.nlm.nih.gov/genome/52
    https://www.ncbi.nlm.nih.gov/genome/assembly/7358741
    https://www.ncbi.nlm.nih.gov/bioproject/20689

Files included in this directory:

mm39.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.

mm39.fa.masked.gz - "Hard-masked" assembly sequence in one file.
    Repeats are masked by capital Ns; non-repeating sequence is shown in
    upper case.

mm39.2bit - contains the complete mouse/mm39 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.soe.ucsc.edu/admin/exe/linux.x86_64/
    See also:
        http://genome.ucsc.edu/admin/git.html
	http://genome.ucsc.edu/admin/jk-install.html

mm39.chrom.sizes - Two-column tab-separated text file containing assembly
    sequence names and sizes.

mm39.agp.gz - Description of how the assembly was generated from
    fragments.

mm39.chromFa.tar.gz - gzipped tar file with each chromosome sequence
    in a separate file, masked as described above for mm39.fa.gz
    To extract the files into a directory:  tar xvzf mm39.chromFa.tar.gz

mm39.fa.out.gz - RepeatMasker .out file.  RepeatMasker was run with the
    -s (sensitive) setting.
    February 01 2017 (open-4-0-8) 1.332 version of RepeatMasker
    RepBase library: Dfam_Consensus RELEASE 20181026
CC    RepBase RELEASE 20181026;                                   *

mm39.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 - Mouse 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 - Mouse mRNA from GenBank. This sequence data is updated
    once a week via automatic GenBank updates.

refMrna.fa.gz - RefSeq mRNA from the same species as the genome.
    This sequence data is updated once a week via automatic GenBank
    updates.

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.

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.

mm39.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.soe.ucsc.edu
[username: anonymous, password: your email address], then cd to the
directory goldenPath/mm39/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.soe.ucsc.edu/goldenPath/mm39/bigZips/ .
For a single file, e.g. chromFa.tar.gz
    rsync -avzP 
        rsync://hgdownload.soe.ucsc.edu/goldenPath/mm39/bigZips/chromFa.tar.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.soe.ucsc.edu/goldenPath/mm39/bigZips/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.soe.ucsc.edu/goldenPath/mm39/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

-----------------------------------------------------------------------------
GenBank Data Usage

The GenBank database is designed to provide and encourage access within
the scientific community to the most up to date and comprehensive DNA
sequence information. Therefore, NCBI places no restrictions on the use
or distribution of the GenBank data. However, some submitters may claim
patent, copyright, or other intellectual property rights in all or a
portion of the data they have submitted. NCBI is not in a position to
assess the validity of such claims, and therefore cannot provide comment
or unrestricted permission concerning the use, copying, or distribution
of the information contained in GenBank.
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      Name                    Last modified      Size  Description
Parent Directory - upstream5000.fa.gz 10-Sep-2020 12:36 35M upstream2000.fa.gz 10-Sep-2020 12:36 15M upstream1000.fa.gz 10-Sep-2020 12:36 8.0M mm39.trf.bed.gz 10-Sep-2020 12:19 19M mm39.fa.out.gz 10-Sep-2020 12:19 161M mm39.fa.masked.gz 10-Sep-2020 12:35 481M mm39.fa.gz 10-Sep-2020 12:29 830M mm39.chromFa.tar.gz 10-Sep-2020 15:03 830M mm39.chrom.sizes 27-Jul-2020 12:46 1.3K mm39.agp.gz 10-Sep-2020 12:18 445K mm39.2bit 30-Jul-2020 09:03 681M md5sum.txt 10-Sep-2020 15:04 550 genes/ 07-Oct-2020 15:48 -