Introduction
^^^^^^^^^^^^

This directory contains the Dec. 2011 (GRCm38/mm10) assembly of the mouse genome
(mm10, Genome Reference Consortium Mouse Build 38 (GCA_000001635.2)), as well
as repeat annotations and GenBank sequences.

This assembly was produced by the Mouse Genome Sequencing Consortium,
and the National Center for Biotechnology Information (NCBI).
For more information on the mouse genome, see the project website:

See also: http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/mouse/
          http://www.ncbi.nlm.nih.gov/genome/52

Analysis set
^^^^^^^^^^^^

NCBI also provides genome files for the GRCm38/mm10 assembly optimized for use
by various Next Generation Sequence read alignment pipelines.  They remove or
annotate alternate sequences which is especially important for variant calling. 

This includes index files generated by BWA, Samtools, Bowtie and HISAT2.

For this set, see: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/

For the background of why it is important to modify genomes for NGS alignment,
on the example of the hg38 assembly, see 
https://software.broadinstitute.org/gatk/documentation/article?id=11010

Files
^^^^^

Files included in this directory:

mm10.2bit - contains the complete mouse/mm10 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

chromAgp.tar.gz - Description of how the assembly was generated from
    fragments, unpacking to one file per chromosome.

chromFa.tar.gz - The assembly sequence in one file per chromosome.
    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.

chromFaMasked.tar.gz - The assembly sequence in one file per chromosome.
    Repeats are masked by capital Ns; non-repeating sequence is shown in
    upper case.

chromOut.tar.gz - RepeatMasker .out files (one file per chromosome).
    RepeatMasker was run with the -s (sensitive) setting.
    Repeat Masker library RELEASE 20110920
    April 26 2011 (open-3-3-0) version of RepeatMasker

chromTrf.tar.gz - Tandem Repeats Finder locations, filtered to keep repeats
    with period less than or equal to 12, and translated into UCSC's BED 5+
    format (one file per chromosome).

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.

mm10.chrom.sizes - Two-column tab-separated text file containing assembly
    sequence names and sizes.

mm10.gc5Base.wigVarStep.gz - ascii data wiggle variable step values used
                           - to construct the GC Percent track
mm10.gc5Base.wig.gz - database table for the GC Percent track
mm10.gc5Base.wib    - binary data to correspond with the gc5Base.wig file

------------------------------------------------------------------
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/mm10/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/mm10/bigZips/ .
For a single file, e.g. chromFa.tar.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/mm10/bigZips/chromFa.tar.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/mm10/bigZips/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/mm10/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

------------------------------------------------------------------
This file last updated: 2012-02-09 - 09 February 2012
------------------------------------------------------------------
      Name                       Last modified      Size  Description
Parent Directory - xenoRefMrna.fa.gz.md5 14-Oct-2019 17:12 52 xenoRefMrna.fa.gz 14-Oct-2019 17:12 287M xenoMrna.fa.gz.md5 14-Oct-2019 17:04 49 xenoMrna.fa.gz 14-Oct-2019 17:04 6.5G upstream5000.fa.gz.md5 14-Oct-2019 17:13 53 upstream5000.fa.gz 14-Oct-2019 17:13 37M upstream2000.fa.gz.md5 14-Oct-2019 17:13 53 upstream2000.fa.gz 14-Oct-2019 17:13 15M upstream1000.fa.gz.md5 14-Oct-2019 17:13 53 upstream1000.fa.gz 14-Oct-2019 17:13 7.8M refMrna.fa.gz.md5 14-Oct-2019 17:12 48 refMrna.fa.gz 14-Oct-2019 17:12 44M mrna.fa.gz.md5 14-Oct-2019 16:53 45 mrna.fa.gz 14-Oct-2019 16:53 261M mm10.gc5Base.wigVarStep.gz 06-Feb-2012 11:55 1.3G mm10.gc5Base.wig.gz 17-Jan-2019 14:10 9.5M mm10.gc5Base.wib 17-Jan-2019 14:10 506M mm10.fa.gz 23-Jan-2020 02:22 830M mm10.chrom.sizes 06-Feb-2012 11:46 1.4K mm10.2bit 07-Feb-2012 10:52 682M md5sum.txt 09-Feb-2012 14:20 457 genes/ 05-Feb-2020 13:47 - est.fa.gz.md5 14-Oct-2019 17:11 44 est.fa.gz 14-Oct-2019 17:11 788M chromTrf.tar.gz 09-Feb-2012 14:02 19M chromOut.tar.gz 09-Feb-2012 13:41 155M chromFaMasked.tar.gz 09-Feb-2012 14:02 479M chromFa.tar.gz 09-Feb-2012 13:54 830M chromAgp.tar.gz 09-Feb-2012 13:40 9.7K