This directory contains the Nov. 2011 (ICGSC Gallus_gallus-4.0/galGal4) assembly of the chicken genome
(galGal4, ICGSC Gallus_gallus-4.0 (GCA_000002315.2)), as well as repeat annotations and GenBank sequences.

For more information about this assembly, please note the NCBI resources:
    http://www.ncbi.nlm.nih.gov/genome/111
    http://www.ncbi.nlm.nih.gov/genome/assembly/317958
    http://www.ncbi.nlm.nih.gov/bioproject/13342

Files included in this directory:

galGal4.2bit - contains the complete chicken/galGal4 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

galGal4.agp.gz - Description of how the assembly was generated from
    fragments.

galGal4.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.

galGal4.fa.masked.gz - "Hard-masked" assembly sequence in one file.
    Repeats are masked by capital Ns; non-repeating sequence is shown in
    upper case.

galGal4.fa.out.gz - RepeatMasker .out file.  RepeatMasker was run with the
    -s (sensitive) setting.  April 26 2011 (open-3-3-0) version of RepeatMasker,
    RepeatMaskerLib.embl version: CC RELEASE 20110920

galGal4.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 - Chicken 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 - Chicken 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.


galGal4.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/galGal4/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/galGal4/bigZips/ .
For a single file, e.g. chromFa.tar.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/galGal4/bigZips/chromFa.tar.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/galGal4/bigZips/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/galGal4/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

------------------------------------------------------------------
The Chicken sequence is made freely available to the community by the
Genome Sequencing Center, Washington University School of Medicine, with
the following understanding:

1. The data may be freely downloaded, used in analyses, and repackaged in
   databases.

2. Users are free to use the data in scientific papers analyzing these data
   if the providers of these data are properly cited:
   International Chicken Genome Sequencing Consortium.  
   Sequence and comparative analysis of the chicken genome provide unique
   perspectives on vertebrate evolution.
   Nature. 2004 Dec 9;432(7018):695-716.  PMID: 15592404
   See http://genome.ucsc.edu/goldenPath/credits.html for credit information.

3. Any redistribution of the data should carry this notice.

------------------------------------------------------------------
[ICO]NameLast modifiedSizeDescription

[DIR]Parent Directory  -  
[TXT]README.txt20-Feb-2015 15:32 5.0K 
[   ]galGal4.2bit05-Jan-2012 10:17 296M 
[   ]galGal4.agp.gz25-May-2012 14:53 238K 
[   ]galGal4.chrom.sizes04-Jan-2012 14:35 379K 
[   ]galGal4.fa.gz25-May-2012 15:01 330M 
[   ]galGal4.fa.masked.gz25-May-2012 15:07 273M 
[   ]galGal4.fa.out.gz25-May-2012 14:53 16M 
[   ]galGal4.trf.bed.gz25-May-2012 14:53 1.5M 
[TXT]md5sum.txt25-May-2012 15:11 463  
[   ]upstream1000.fa.gz25-May-2012 15:10 1.2M 
[   ]upstream2000.fa.gz25-May-2012 15:11 2.4M 
[   ]upstream5000.fa.gz25-May-2012 15:11 5.7M 

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