This directory contains the Build 36.1 finished human genome assembly
(hg18, Mar. 2006). The chromosomal sequences were assembled by
the International Human Genome Project sequencing centers. 

Files included in this directory:

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. Repeat masking was done using the following
    RepeatMasker/RepBase versions: RepBase Update 9.11, RM database 
    version 20050112. 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.

chromOut.RM3.2.7.zip - RepeatMasker (v3.2.7) .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.  

hg18.2bit - hg18.2bit contains the complete hg18 Human 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.

hg18.RM.tbl.tar.gz - the RepeatMasker .tbl file output.  Each file
    in this tar file is for one chunk of contig sequence used during
    the RepeatMasker operation, for example:
	1/NT_004321/NT_004321_0.fa.tbl
    There are 5990 of these chunks of contig sequences, their coordinate
    coorrespondence to contig coordinates can be found in the
    hg18.RM.lft.tar.gz lift files.

hg18.RM.lft.tar.gz - lift files to lift the hg18.RM.tbl coordinates to
    contig coordinates.

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

-----------------------------------------------------------------
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 hgdownload.cse.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/hg18/bigZips

To download multiple files from the UNIX command line, use the "mget" command. 
    mget <filename1> <filename2> ...
    - or -
    mget -a (to download all the files in the directory) 
Use the "prompt" command to toggle the interactive mode if you do not want 
to be prompted for each file that you download.

All the files in this directory are freely available for public use.
[ICO]NameLast modifiedSizeDescription

[DIR]Parent Directory  -  
[TXT]README.txt20-Feb-2015 15:32 5.0K 
[TXT]README.txt.bak05-Feb-2009 10:26 5.0K 
[   ]chromAgp.zip06-Apr-2006 09:45 537K 
[   ]chromFa.zip03-Feb-2006 11:05 899M 
[   ]chromFaMasked.zip03-Feb-2006 11:12 487M 
[   ]chromOut.RM3.2.7.zip05-Feb-2009 10:10 162M 
[   ]chromOut.zip03-Feb-2006 10:51 153M 
[   ]chromTrf.zip03-Feb-2006 11:35 6.8M 
[   ]contigAgp.zip03-Feb-2006 11:12 596K 
[   ]contigFa.zip03-Feb-2006 11:27 898M 
[   ]contigFaMasked.zip03-Feb-2006 11:35 488M 
[   ]contigOut.zip03-Feb-2006 11:14 152M 
[   ]contigTrf.zip03-Feb-2006 11:35 7.0M 
[   ]hg18.2bit20-Dec-2005 10:33 770M 
[   ]hg18.2bit.zip03-Feb-2006 15:28 671M 
[   ]hg18.RM.lft.tar.gz10-Nov-2008 14:08 41K 
[   ]hg18.RM.tbl.tar.gz10-Nov-2008 13:55 1.3M 
[   ]hg18.chrom.sizes06-Dec-2005 16:34 855  
[   ]liftAll.zip03-Feb-2006 11:35 5.5K 
[TXT]md5sum.txt05-Feb-2009 10:25 734  
[   ]upstream1000.zip06-Apr-2006 10:42 6.2M 
[   ]upstream2000.zip06-Apr-2006 10:43 12M 
[   ]upstream5000.zip06-Apr-2006 10:50 28M 

Apache/2.2.15 (CentOS) Server at hgdownload-test.sdsc.edu Port 80