This directory contains the v.1.0 Mmul_051212 rhesus genome assembly 
(rheMac2, Jan. 2006) produced by the Baylor College of Medicine Human 
Genome Sequencing Center.  For more information about these data, see the 
Baylor web page at http://www.hgsc.bcm.tmc.edu/projects/rmacaque/.

Files included in this directory:

rheMac2.2bit - contains the complete rhesus/rheMac2 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

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

md5sum.txt - MD5 checksum of these files to verify correct transmission.

mrna.fa.gz - Rhesus macaque 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.

chromFa.tar.gz - The assembly sequence in one file per chromosome.
    Repeats from RepeatMasker and Tandem Repeats Finder are shown in 
    lower case; non-repeating sequence is shown in upper case.  
    RepeatMasker 19 Jan 2006 version with RepBase libraries: RepBase 
    Update 9.11,  RM database version 20060120.
    NOTE: In most assemblies, Tandem Repeats Finder repeats were 
    filtered to retain only the repeats with period <= 12.  However,
    the filtering was omitted for this assembly, so the lower case 
    masking includes all repeats.

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 file for chromosomes. These were 
    created by RepeatMasker at the -s sensitive setting.

chromTrf.tar.gz - Tandem Repeats Finder locations, translated into one
    .bed file per chromosome. 
    NOTE: In most assemblies, Tandem Repeats Finder repeats were 
    filtered to retain only the repeats with period <= 12.  However,
    the filtering was omitted for this assembly, so these files contain
    all Tandem Repeats Finder results.

rheMac2.agp.tar.gz - Description of how the assembly was generated from
     fragments. 

rheMac2.qual.qv.gz - base by base qual scores for rheMac2 assembly.
    Values vary from 0 to 60.

upstream1000.fa.gz - Sequences 1000 bases upstream of annotated
    transcription starts for RefSeq genes with annotated 5' UTRs.  
    This file is updated weekly so it could 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.
    
v1.edit3.noContam.ctg.fasta.gz - The unmasked contigs fasta from the assembly.

v1.edit3.noContam.ctg.qv.gz - The per base quality scores from contigs 
    sequences. 

v1_edit4.scf.fasta.gz - The sequences for the large scaffolds that were
    using in the assembly.


rheMac2.chrom.sizes - Two-column tab-separated text file containing assembly
    sequence names and sizes.

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If you plan to download a large file or multiple files from this 
directory, we recommend you use ftp rather than downloading the files 
via our website. To do so, ftp to hgdownload.cse.ucsc.edu, then go to 
the directory goldenPath/rheMac2/bigZips. To download multiple files, use
the "mget" command:

    mget <filename1> <filename2> ...
    - or -
    mget -a (to download all the files in the directory)

Please review the restrictions on the use of the rhesus assembly data at
http://genome.ucsc.edu/goldenPath/credits.html#rhesus_use.