This directory contains the Build 34 finished human genome
assembly (hg16, Jul. 2003).  The chromosomal sequences were 
assembled by the International Human Genome Project sequencing 
centers and verified by NCBI and UCSC. The annotations are from 
UCSC and collaborators worldwide.

Files included in this directory:

hg16.2bit - contains the complete human/hg16 genome sequence
    in the 2bit file format.  While we are providing the .2bit for
    this assembly, we will continue to use the .nib files in
    the Genome Browser.  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

chromAgp.zip - Description of how the assembly was generated,
     unpacking to one file per chromosome.  

chromFa.zip - The assembly sequence in one file per chromosome.
    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 main assembly is found in the chrN.fa
    files, where N is the name of the chromosome. The chrN_random.fa
    files contain clones that are not yet finished or cannot be placed
    with certainty at a specific place on the chromosome. In some
    cases, including the human HLA region on chromosome 6, the
    chrN_random.fa files also contain haplotypes that differ from the
    main assembly.

chromFaMasked.zip - The assembly sequence in one file per 
    chromosome. Repeats are masked by capital Ns; non-repeating 
    sequence is shown in upper case.  

chromOut.zip - RepeatMasker .out file for chromosomes. These were 
    created by RepeatMasker at the -s sensitive setting.

chromTrf.zip - Tandem Repeats Finder locations, filtered to keep 
    repeats with period of less than or equal to 12, and translated 
    into one .bed file per chromosome.  

contigAgp.zip - Description of how the assembly was generated 
    from fragments at a contig layout level. 

contigFa.zip - The assembly sequence contigs, in one file per NCBI contig.  
    All contigs are in forward orientation relative to the chromosome. 
    In some cases, this means that contigs will be reversed relative to 
    their orientation in the NCBI assembly. Repeats from RepeatMasker 
    and Tandem Repeats Finder are shown in lower case; non-repeating 
    sequence is shown in upper case.

contigFaMasked.zip - The assembly sequence contigs, in one file per 
    contig. Repeats are masked by capital Ns; non-repeating sequence 
    is shown in upper case.  

contigOut.zip - RepeatMasker .out file for contigs.  These were 
    created by RepeatMasker at the -s sensitive setting.

contigTrf.zip - Tandem Repeats Finder locations, filtered to keep 
    repeats with period less than or equal to 12, and translated into 
    one .bed file per contig.  

est.fa.gz - Human ESTs from GenBank.
    This sequence data is updated once a week via automatic GenBank 
    updates.

liftAll.zip - Offsets of contigs within chromosomes.

mrna.fa.gz - Human 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 for RefSeq genes with annotated 5' UTRs.  
    This file is updated weekly so it could be slightly out      
    of sync with the RefSeq data which is updated daily for most
    assemblies.

upstream2000.zip - Same as upstream1000, but 2000 bases.

upstream5000.zip - Same as upstream1000, but 5000 bases.

xenoMrna.fa.gz - All GenBank mRNAs from species other than that of 
    the genome. This sequence data is updated once a week via automatic 
    GenBank updates.


hg16.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, then 
go to the directory goldenPath/hg16/bigZips. To download multiple 
files, use the "mget" command:

    mget <filename1> <filename2> ...
    - or -
    mget -a (to download all the files in the directory) 
 
All files in this directory are freely available for public use.
[ICO]NameLast modifiedSizeDescription

[DIR]Parent Directory  -  
[TXT]README.txt20-Feb-2015 15:32 4.8K 
[TXT]README.txt.bak06-May-2014 16:07 4.7K 
[   ]hg16.2bit20-Jun-2005 07:22 768M 
[   ]hg16.2bit.md507-May-2014 15:22 44  
[   ]hg16.chrom.sizes05-Aug-2003 10:42 713  

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