This directory contains the Jul. 2010 (Zv9/danRer7) assembly of
the zebrafish genome
(danRer7, Wellcome Trust Sanger Institute Zv9 (GCA_000002035.2)),
as well as repeat annotations and GenBank sequences.

This assembly was produced by a collaboration between the
Wellcome Trust Sanger Institute in Cambridge, UK, the Max Planck Institute
for Developmental Biology in Tuebingen, Germany, the Netherlands Institute
for Developmental Biology (Hubrecht Laboratory), Utrecht, The Netherlands
and Yi Zhou and Leonard Zon from the Children's Hospital in Boston,
Massachusetts..
For more information on the zebrafish genome, see the project website:

    http://www.sanger.ac.uk/Projects/D_rerio/

Files included in this directory:

danRer7.2bit - contains the complete zebrafish/danRer7 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

danRer7.agp.gz - Description of how the assembly was generated from
    fragments.

danRer7.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.

danRer7.fa.masked.gz - "Hard-masked" assembly sequence in one file.
    Repeats are masked by capital Ns; non-repeating sequence is shown in
    upper case.

danRer7.fa.out.gz - RepeatMasker .out file.  RepeatMasker was run with the
    -s (sensitive) setting.  Repeat Masker version: June 30 2010 (open-3-2-9)
	with library version 20090604

danRer7.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 - Zebrafish 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 - Zebrafish 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.

danRer7.chrom.sizes - Two-column tab-separated text file containing assembly
    sequence names and sizes.

danRer7.gc5Base.wigVarStep.gz - ascii data wiggle variable step values used
                           - to construct the GC Percent track
danRer7.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
danRer7.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

danRer7.chromAlias.txt - sequence name alias file, one line
    for each sequence name.  First column is sequence name followed by
    tab separated alias names.

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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/danRer7/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/danRer7/bigZips/ .
For a single file, e.g. chromFa.tar.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/danRer7/bigZips/chromFa.tar.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/danRer7/bigZips/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/danRer7/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