This directory contains the Mar. 2012 (RGSC 5.0/rn5) assembly of the rat genome
(rn5, RGSC Rnor_5.0 (GCA_000001895.3)), as well as repeat annotations and
GenBank sequences.

For more information about this assembly, please note the NCBI resources:
    http://www.ncbi.nlm.nih.gov/genome/73
    http://www.ncbi.nlm.nih.gov/genome/assembly/382928
    http://www.ncbi.nlm.nih.gov/bioproject/16219

Files included in this directory:

rn5.2bit - contains the complete rat/rn5 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

rn5.agp.gz - Description of how the assembly was generated from
    fragments.

rn5.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.

chromFa.tar.gz - the same "Soft-masked" sequence from rn5.fa.gz in a
    tar file image.  Unpacks to create a directory ./rn5/ with 2.739 files,
    one for each sequence in the assembly

rn5.fa.masked.gz - "Hard-masked" assembly sequence in one file.
    Repeats are masked by capital Ns; non-repeating sequence is shown in
    upper case.

rn5.fa.out.gz - RepeatMasker .out file.  RepeatMasker was run with the
    -s (sensitive) setting.  Repeat Masker version: April 26 2011 (open-3-3-0)
    database version: RELEASE 20110920

rn5.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 - Rat 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 - Rat 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.


rn5.chrom.sizes - Two-column tab-separated text file containing assembly
    sequence names and sizes.

rn5.gc5Base.wigVarStep.gz - ascii data wiggle variable step values used
                           - to construct the GC Percent track
rn5.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
rn5.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

rn5.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/rn5/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/rn5/bigZips/ .
For a single file, e.g. chromFa.tar.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/rn5/bigZips/chromFa.tar.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/rn5/bigZips/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/rn5/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

------------------------------------------------------------------
These data are  made 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 this data (the Rat
   Genome Sequencing Consortium) are properly acknowledged.
3. The Centers producing the data reserve the right to publish the
   initial large-scale analyses of the dataset, 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. This is in accordance with, and with the understandings in the Fort
   Lauderdale meeting discussing Community Resource Projects (see
   http://www.wellcome.ac.uk/en/1/awtpubrepdat.html) and the resulting
   NHGRI policy statement
   (http://www.genome.gov/page.cfm?pageID=10506537).
5. Any redistribution of the data should carry this notice.
      Name                      Last modified      Size  Description
Parent Directory - chromFa.tar.gz 2012-10-09 15:45 809M est.fa.gz 2019-10-17 20:06 208M est.fa.gz.md5 2019-10-17 20:06 44 genes/ 2020-02-05 13:47 - md5sum.txt 2019-01-17 15:58 651 mrna.fa.gz 2019-10-17 19:50 25M mrna.fa.gz.md5 2019-10-17 19:50 45 refMrna.fa.gz 2019-10-17 20:06 15M refMrna.fa.gz.md5 2019-10-17 20:06 48 rn5.2bit 2012-03-23 09:34 725M rn5.agp.gz 2012-05-09 16:25 2.9M rn5.chrom.sizes 2012-03-19 11:36 69K rn5.chromAlias.txt 2020-09-29 10:49 5.4K rn5.fa.gz 2012-05-09 16:39 809M rn5.fa.masked.gz 2012-05-09 16:47 484M rn5.fa.out.gz 2012-05-09 16:26 146M rn5.gc5Base.wib 2019-01-17 14:53 498M rn5.gc5Base.wig.gz 2019-01-17 14:53 10M rn5.gc5Base.wigVarStep.gz 2012-03-19 11:46 1.3G rn5.trf.bed.gz 2012-05-09 16:26 16M upstream1000.fa.gz 2019-10-17 20:07 4.0M upstream1000.fa.gz.md5 2019-10-17 20:07 53 upstream2000.fa.gz 2019-10-17 20:07 7.7M upstream2000.fa.gz.md5 2019-10-17 20:07 53 upstream5000.fa.gz 2019-10-17 20:07 18M upstream5000.fa.gz.md5 2019-10-17 20:07 53 xenoMrna.fa.gz 2019-10-17 20:00 6.8G xenoMrna.fa.gz.md5 2019-10-17 20:00 49 xenoRefMrna.fa.gz 2019-10-17 20:06 316M xenoRefMrna.fa.gz.md5 2019-10-17 20:06 52