This directory contains the Oct. 2011 (FUGU5/fr3) assembly of the fugu genome
(fr3, Fugu Genome Sequencing Consortium - FUGU5
(NCBI project 1434, GCA_000180615.2)),
as well as repeat annotations and GenBank sequences.

This assembly was produced by the Fugu Genome Sequencing Consortium,
               http://www.fugu-sg.org/
as part of the International Fugu Genome Consortium, led by JGI and the
Singapore Institute of Molecular and Cell Biology (IMCB).

For more information on the fugu genome, see the project website:
       http://www.fugu-sg.org/

Files included in this directory:

fr3.2bit - contains the complete fugu/fr3 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

fr3.agp.gz - Description of how the assembly was generated from
    fragments.

fr3.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.

fr3.fa.masked.gz - "Hard-masked" assembly sequence in one file.
    Repeats are masked by capital Ns; non-repeating sequence is shown in
    upper case.

fr3.fa.out.gz - RepeatMasker .out file.  RepeatMasker was run with the
    -s (sensitive) setting.  RepeatMasker version: April 26 2011 (open-3-3-0)
    with library version: RELEASE 20110920

fr3.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 - Fugu 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 - Fugu 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.


fr3.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/fr3/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/fr3/bigZips/ .
For a single file, e.g. chromFa.tar.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/fr3/bigZips/chromFa.tar.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/fr3/bigZips/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/fr3/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

==============================================================================

1.  These data have been freely provided by the JGI for use in the
        UCSC Genome Browser.

==============================================================================
[ICO]NameLast modifiedSizeDescription

[DIR]Parent Directory  -  
[TXT]README.txt20-Feb-2015 15:32 4.5K 
[   ]fr3.2bit17-Nov-2011 11:51 107M 
[   ]fr3.agp.gz23-Feb-2012 15:16 417K 
[   ]fr3.chrom.sizes16-Nov-2011 11:29 95K 
[   ]fr3.fa.gz23-Feb-2012 15:18 112M 
[   ]fr3.fa.masked.gz23-Feb-2012 15:19 94M 
[   ]fr3.fa.out.gz23-Feb-2012 15:16 5.5M 
[   ]fr3.trf.bed.gz23-Feb-2012 15:16 1.5M 
[TXT]md5sum.txt23-Feb-2012 15:20 439  
[   ]upstream1000.fa.gz23-Feb-2012 15:20 70K 
[   ]upstream2000.fa.gz23-Feb-2012 15:20 133K 
[   ]upstream5000.fa.gz23-Feb-2012 15:20 320K 

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