This directory contains the Dec. 2008 assembly of the zebrafish genome
(danRer6, Wellcome Trust Sanger Institute, Zv8 assembly (CAAK00000000.5)), 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:

danRer6.agp.gz - Description of how the assembly was generated from
    fragments.

danRer6.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.

danRer6.fa.masked.gz - "Hard-masked" assembly sequence in one file.
    Repeats are masked by capital Ns; non-repeating sequence is shown in
    upper case.

danRer6.fa.out.gz - RepeatMasker .out file.  RepeatMasker was run with the
    -s (sensitive) setting.  *** PLEASE ADD REPEATMASKER VERSION AND LIB VERSION FROM THE DATE THAT REPEATMASKER WAS RUN (MAY BE IN MAKE.DOC)

danRer6.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.

danRer6.2bit - contains the complete danRer6 Zebrafish Genome
    in the 2bit format.  A utility program, twoBitToFa (available
    from our src tree), can be used to extract .fa file(s) from
    this file.  See also:
        http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/

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.

danRer6.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/danRer6/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/danRer6/bigZips/ .
For a single file, e.g. chromFa.tar.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/danRer6/bigZips/chromFa.tar.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/danRer6/bigZips/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/danRer6/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 4.1K 
[   ]danRer6.2bit06-Jul-2009 13:41 381M 
[   ]danRer6.agp.gz08-Jul-2009 13:37 1.5M 
[   ]danRer6.chrom.sizes24-Jun-2009 14:41 188K 
[   ]danRer6.fa.gz08-Jul-2009 13:59 463M 
[   ]danRer6.fa.masked.gz08-Jul-2009 14:04 240M 
[   ]danRer6.fa.out.gz08-Jul-2009 13:48 117M 
[   ]danRer6.trf.bed.gz08-Jul-2009 13:49 9.1M 
[TXT]md5sum.txt25-Jan-2010 15:41 463  
[   ]upstream1000.fa.gz08-Jul-2009 14:16 3.7M 
[   ]upstream2000.fa.gz08-Jul-2009 14:17 7.0M 
[   ]upstream5000.fa.gz08-Jul-2009 14:18 17M 

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