This directory contains the Feb. 2010 (ISGC Ovis_aries_1.0/oviAri1) assembly of the sheep genome
(oviAri1, ISGC (NCBI project 10709, accession GCA_000005525.1)), as well as repeat annotations and GenBank sequences.

This assembly was produced by the International Sheep Genomics Consortium
(ISGC).
For more information on the sheep genome, see the project website:
http://www.sheephapmap.org/
http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=33937

Files included in this directory:

oviAri1.2bit - contains the complete sheep/oviAri1 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

oviAri1.agp.gz - Description of how the assembly was generated from
    fragments.

oviAri1.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.

oviAri1.fa.masked.gz - "Hard-masked" assembly sequence in one file.
    Repeats are masked by capital Ns; non-repeating sequence is shown in
    upper case.

oviAri1.fa.out.gz - RepeatMasker .out file.  RepeatMasker was run with the
    -s (sensitive) setting.  
    June 4 2009 (open-3-2-8) version of RepeatMasker
    RepeatMaskerLib.embl version: 20090604;

oviAri1.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 - Sheep 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 - Sheep 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.

oviAri1.chrom.sizes - Two-column tab-separated text file containing assembly
    sequence names and sizes.

------------------------------------------------------------------
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/oviAri1/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/oviAri1/bigZips/ .
For a single file, e.g. chromFa.tar.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/oviAri1/bigZips/chromFa.tar.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/oviAri1/bigZips/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/oviAri1/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


[ICO]NameLast modifiedSizeDescription

[DIR]Parent Directory  -  
[TXT]README.txt20-Feb-2015 15:32 3.7K 
[TXT]md5sum.txt02-Apr-2012 09:22 304  
[   ]oviAri1.2bit14-Apr-2010 19:15 718M 
[   ]oviAri1.agp.gz07-Feb-2011 09:40 60M 
[   ]oviAri1.chrom.sizes14-Apr-2010 15:55 25K 
[   ]oviAri1.fa.gz07-Feb-2011 09:47 426M 
[   ]oviAri1.fa.masked.gz07-Feb-2011 09:53 337M 
[   ]oviAri1.fa.out.gz07-Feb-2011 09:41 61M 
[   ]oviAri1.trf.bed.gz07-Feb-2011 09:41 501K 

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