This directory contains the May 2011 (gorGor3.1/gorGor3) assembly of the
gorilla genome (gorGor3, Wellcome Trust Sanger Institute May 2011
(NCBI project 31265, GCA_000151905.1)), as well as repeat annotations
and GenBank sequences.
This assembly was produced by the Wellcome Trust Sanger Institute.
For more information on the gorilla genome, see the project website:
http://www.sanger.ac.uk/resources/downloads/gorilla/
See also, the WGS records: http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=CABD02
Files included in this directory:
gorGor3.2bit - contains the complete gorilla/gorGor3 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
gorGor3.agp.gz - Description of how the assembly was generated from
fragments.
gorGor3.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.
gorGor3.fa.masked.gz - "Hard-masked" assembly sequence in one file.
Repeats are masked by capital Ns; non-repeating sequence is shown in
upper case.
gorGor3.fa.out.gz - RepeatMasker .out file. RepeatMasker was run with the
-s (sensitive) setting. April 26 2011 (open-3-3-0) version of RepeatMasker
with RepeatMaskerLib.embl RELEASE 20110920
gorGor3.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.
md5sum.txt - checksums of files in this directory
mrna.fa.gz - Gorilla mRNA from GenBank. This sequence data is updated
once a week via automatic GenBank updates.
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.
gorGor3.chrom.sizes - Two-column tab-separated text file containing assembly
sequence names and sizes.
gorGor3.gc5Base.wigVarStep.gz - ascii data wiggle variable step values used
- to construct the GC Percent track
gorGor3.gc5Base.wig.gz - wiggle database table for the GC Percent track
- this is an older standard alternative to the current
- bigWig format of the track, sometimes usefull for analysis
gorGor3.gc5Base.wib - binary data to correspond with the gc5Base.wig file
see also: http://genome.ucsc.edu/goldenPath/help/wiggle.html
and http://genomewiki.ucsc.edu/index.php/Using_hgWiggle_without_a_database
for a discussion of how to use the wig.gz and .wib files for
interaction with the GC percent data values
gorGor3.chromAlias.txt - sequence name alias file, one line
for each sequence name. First column is sequence name followed by
tab separated alias names.
------------------------------------------------------------------
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/gorGor3/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/gorGor3/bigZips/ .
For a single file, e.g. chromFa.tar.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/gorGor3/bigZips/chromFa.tar.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/gorGor3/bigZips/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/gorGor3/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
------------------------------------------------------------------
Please note the following data sharing guidelines:
http://www.sanger.ac.uk/datasharing/
Name Last modified Size Description
Parent Directory -
gorGor3.chrom.sizes 2011-10-11 14:51 800K
gorGor3.gc5Base.wigVarStep.gz 2011-10-11 15:47 1.4G
gorGor3.2bit 2011-10-14 15:13 758M
gorGor3.agp.gz 2011-11-14 10:44 739K
gorGor3.fa.out.gz 2011-11-14 10:45 158M
gorGor3.trf.bed.gz 2011-11-14 10:45 6.0M
gorGor3.fa.gz 2011-11-14 10:59 867M
gorGor3.fa.masked.gz 2011-11-14 11:06 468M
gorGor3.gc5Base.wib 2019-01-17 14:49 559M
gorGor3.gc5Base.wig.gz 2019-01-17 14:49 13M
md5sum.txt 2019-01-17 15:54 479
mrna.fa.gz 2019-10-17 05:35 108K
mrna.fa.gz.md5 2019-10-17 05:35 45
xenoMrna.fa.gz 2019-10-17 05:45 6.8G
xenoMrna.fa.gz.md5 2019-10-17 05:46 49
xenoRefMrna.fa.gz 2019-10-17 05:46 331M
xenoRefMrna.fa.gz.md5 2019-10-17 05:46 52
upstream1000.fa.gz 2019-10-17 05:47 3.5M
upstream1000.fa.gz.md5 2019-10-17 05:47 53
upstream2000.fa.gz 2019-10-17 05:47 6.7M
upstream2000.fa.gz.md5 2019-10-17 05:47 53
upstream5000.fa.gz 2019-10-17 05:48 16M
upstream5000.fa.gz.md5 2019-10-17 05:48 53
genes/ 2020-02-05 13:47 -
gorGor3.chromAlias.txt 2022-09-08 14:12 221
gorGor3.chromAlias.bb 2022-09-08 14:12 31K