This directory contains the Feb. 2009 assembly of the human genome (hg19,
GRCh37 Genome Reference Consortium Human Reference 37 (GCA_000001405.1)),
as well as repeat annotations and GenBank sequences.

The Feb. 2009 human reference sequence (GRCh37) was produced by the
Genome Reference Consortium:
	http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/

Note on chrM:
Since the release of the UCSC hg19 assembly, the Homo sapiens mitochondrion
sequence (represented as "chrM" in the Genome Browser) has been replaced in
GenBank with the record NC_012920. We have not replaced the original sequence,
NC_001807, in the hg19 Genome Browser. We plan to use the Revised Cambridge
Reference Sequence (rCRS, http://mitomap.org/bin/view.pl/MITOMAP/HumanMitoSeq)
in the next human assembly release.

Files included in this directory:

chromAgp.tar.gz - Description of how the assembly was generated from
    fragments, unpacking to one file per chromosome.

chromFa.tar.gz - 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.

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

chromOut.tar.gz - RepeatMasker .out files (one file per chromosome).
    RepeatMasker was run with the -s (sensitive) setting.
    Using: Jan 29 2009 (open-3-2-7) version of RepeatMasker and
    RELEASE 20090120 of library RepeatMaskerLib.embl

chromTrf.tar.gz - Tandem Repeats Finder locations, filtered to keep repeats
    with period less than or equal to 12, and translated into UCSC's BED 5+
    format (one file per chromosome).

hg19.2bit - contains the complete hg19 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.  See also:
	http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/

est.fa.gz - Human 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 - 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 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.


hg19.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/hg19/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/hg19/bigZips/ .
For a single file, e.g. chromFa.tar.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/chromFa.tar.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/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

All the files in this directory are freely available for public use.
      Name                    Last modified      Size  Description
Parent Directory - chromAgp.tar.gz 20-Mar-2009 09:02 538K chromFa.tar.gz 20-Mar-2009 09:21 905M chromFaMasked.tar.gz 20-Mar-2009 09:30 477M chromOut.tar.gz 20-Mar-2009 09:03 163M chromTrf.tar.gz 20-Mar-2009 09:30 7.6M est.fa.gz 27-May-2017 21:32 1.5G est.fa.gz.md5 27-May-2017 21:32 44 hg19.2bit 08-Mar-2009 15:29 778M hg19.chrom.sizes 08-Mar-2009 14:56 1.9K md5sum.txt 29-Jul-2009 10:04 457 mrna.fa.gz 27-May-2017 21:09 275M mrna.fa.gz.md5 27-May-2017 21:09 45 refMrna.fa.gz 27-May-2017 21:32 65M refMrna.fa.gz.md5 27-May-2017 21:32 48 upstream1000.fa.gz 27-May-2017 21:33 8.8M upstream1000.fa.gz.md5 27-May-2017 21:33 53 upstream2000.fa.gz 27-May-2017 21:34 17M upstream2000.fa.gz.md5 27-May-2017 21:34 53 upstream5000.fa.gz 27-May-2017 21:35 42M upstream5000.fa.gz.md5 27-May-2017 21:35 53 xenoMrna.fa.gz 27-May-2017 21:21 5.8G xenoMrna.fa.gz.md5 27-May-2017 21:22 49 xenoRefMrna.fa.gz 27-May-2017 21:32 234M xenoRefMrna.fa.gz.md5 27-May-2017 21:32 52