This directory contains the Apr. 2009 (Baylor Btau_4.2/bosTau5) assembly of the cow genome
(Btau_4.2, Baylor (NCBI project 10708, accession GCA_000000095.5)), as well as repeat annotations and GenBank sequences.
This assembly was produced by Baylor College of Medicine Human Genome
Sequencing Center.
For more information on the cow genome, see the project website:
http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=search&term=txid9913
http://genomes.arc.georgetown.edu/drupal/bovine/?q=bovine_genome_consortium
http://www.bcm.edu/news/packages/bovinegenome.cfm
Files included in this directory:
bosTau5.2bit - contains the complete cow/bosTau5 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/cvs.html
http://genome.ucsc.edu/admin/jk-install.html
bosTau5.agp.gz - Description of how the assembly was generated from
fragments.
bosTau5.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.
bosTau5.fa.masked.gz - "Hard-masked" assembly sequence in one file.
Repeats are masked by capital Ns; non-repeating sequence is shown in
upper case.
bosTau5.fa.out.gz - RepeatMasker .out file. RepeatMasker was run with the
-s (sensitive) setting. *** PLEASE ADD REPEATMASKER VERSION AND LIB VERSION FROM THE DATE THAT REPEATMASKER WAS RUN (MAY BE IN MAKE.DOC)
bosTau5.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
bosTau5.chrom.sizes - Two-column tab-separated text file containing assembly
sequence names and sizes.
bosTau5.gc5Base.wigVarStep.gz - ascii data wiggle variable step values used
- to construct the GC Percent track
bosTau5.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
bosTau5.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
------------------------------------------------------------------
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/bosTau5/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/bosTau5/bigZips/ .
For a single file, e.g. chromFa.tar.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/bosTau5/bigZips/chromFa.tar.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/bosTau5/bigZips/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/bosTau5/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
For conditions of use regarding the Cow genome sequence data, see
http://www.hgsc.bcm.tmc.edu/projects/conditions_for_use.html .
Name Last modified Size Description
Parent Directory -
md5sum.txt 2019-01-17 15:51 479
bosTau5.gc5Base.wig.gz 2019-01-17 14:45 11M
bosTau5.gc5Base.wib 2019-01-17 14:45 524M
bosTau5.chrom.sizes 2010-07-19 15:08 263K
bosTau5.gc5Base.wigVarStep.gz 2010-07-13 16:26 1.4G