This directory contains the Mar. 2012 (RGSC 5.0/rn5) assembly of the rat genome
(rn5, RGSC Rnor_5.0 (GCA_000001895.3)), 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/73
http://www.ncbi.nlm.nih.gov/genome/assembly/382928
http://www.ncbi.nlm.nih.gov/bioproject/16219
Files included in this directory:
rn5.2bit - contains the complete rat/rn5 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
rn5.agp.gz - Description of how the assembly was generated from
fragments.
rn5.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.
chromFa.tar.gz - the same "Soft-masked" sequence from rn5.fa.gz in a
tar file image. Unpacks to create a directory ./rn5/ with 2.739 files,
one for each sequence in the assembly
rn5.fa.masked.gz - "Hard-masked" assembly sequence in one file.
Repeats are masked by capital Ns; non-repeating sequence is shown in
upper case.
rn5.fa.out.gz - RepeatMasker .out file. RepeatMasker was run with the
-s (sensitive) setting. Repeat Masker version: April 26 2011 (open-3-3-0)
database version: RELEASE 20110920
rn5.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 - Rat 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 - Rat 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.
rn5.chrom.sizes - Two-column tab-separated text file containing assembly
sequence names and sizes.
rn5.gc5Base.wigVarStep.gz - ascii data wiggle variable step values used
- to construct the GC Percent track
rn5.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
rn5.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
rn5.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/rn5/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/rn5/bigZips/ .
For a single file, e.g. chromFa.tar.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/rn5/bigZips/chromFa.tar.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/rn5/bigZips/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/rn5/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
------------------------------------------------------------------
These data are made available before scientific publication 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
particular genes and regions if the providers of this data (the Rat
Genome Sequencing Consortium) are properly acknowledged.
3. The Centers producing the data reserve the right to publish the
initial large-scale analyses of the dataset, including large-scale
identification of regions of evolutionary conservation and large-scale
genomic assembly. Large-scale refers to regions with size on the order
of a chromosome (that is, 30 Mb or more).
4. This is in accordance with, and with the understandings in the Fort
Lauderdale meeting discussing Community Resource Projects (see
http://www.wellcome.ac.uk/en/1/awtpubrepdat.html) and the resulting
NHGRI policy statement
(http://www.genome.gov/page.cfm?pageID=10506537).
5. Any redistribution of the data should carry this notice.
Name Last modified Size Description
Parent Directory -
rn5.chromAlias.bb 2022-09-08 14:16 68K
rn5.chromAlias.txt 2022-09-08 14:16 5.3K
genes/ 2020-02-05 13:47 -
upstream5000.fa.gz.md5 2019-10-17 20:07 53
upstream5000.fa.gz 2019-10-17 20:07 18M
upstream2000.fa.gz.md5 2019-10-17 20:07 53
upstream2000.fa.gz 2019-10-17 20:07 7.7M
upstream1000.fa.gz.md5 2019-10-17 20:07 53
upstream1000.fa.gz 2019-10-17 20:07 4.0M
refMrna.fa.gz.md5 2019-10-17 20:06 48
refMrna.fa.gz 2019-10-17 20:06 15M
xenoRefMrna.fa.gz.md5 2019-10-17 20:06 52
xenoRefMrna.fa.gz 2019-10-17 20:06 316M
est.fa.gz.md5 2019-10-17 20:06 44
est.fa.gz 2019-10-17 20:06 208M
xenoMrna.fa.gz.md5 2019-10-17 20:00 49
xenoMrna.fa.gz 2019-10-17 20:00 6.8G
mrna.fa.gz.md5 2019-10-17 19:50 45
mrna.fa.gz 2019-10-17 19:50 25M
md5sum.txt 2019-01-17 15:58 651
rn5.gc5Base.wig.gz 2019-01-17 14:53 10M
rn5.gc5Base.wib 2019-01-17 14:53 498M
chromFa.tar.gz 2012-10-09 15:45 809M
rn5.fa.masked.gz 2012-05-09 16:47 484M
rn5.fa.gz 2012-05-09 16:39 809M
rn5.trf.bed.gz 2012-05-09 16:26 16M
rn5.fa.out.gz 2012-05-09 16:26 146M
rn5.agp.gz 2012-05-09 16:25 2.9M
rn5.2bit 2012-03-23 09:34 725M
rn5.gc5Base.wigVarStep.gz 2012-03-19 11:46 1.3G
rn5.chrom.sizes 2012-03-19 11:36 69K