This directory contains the Nov. 2009 (Bos_taurus_UMD_3.1/bosTau6) assembly of the cow genome
(bosTau6, UMD_3.1 (NCBI project 10708, accession GCA_000003055.3)), as well as repeat annotations and GenBank sequences.
This assembly was produced by the National Center for Biotechnology Information (NCBI).
For more information on the cow genome, see the project website:
"http://www.ncbi.nlm.nih.gov/sites/entrez?Db=genomeprj&cmd=ShowDetailView&TermToSearch=10708
Files included in this directory:
bosTau6.2bit - contains the complete cow/bosTau6 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
bosTau6.agp.gz - Description of how the assembly was generated from
fragments.
bosTau6.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.
bosTau6.fa.masked.gz - "Hard-masked" assembly sequence in one file.
Repeats are masked by capital Ns; non-repeating sequence is shown in
upper case.
bosTau6.fa.out.gz - RepeatMasker .out file. RepeatMasker was run with the
-s (sensitive) setting. RepeatMasker version: June 30 2010 (open-3-2-9)
RepeatMasker library version: 20090604
bosTau6.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 - Cow 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 - Cow 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.
bosTau6.chrom.sizes - Two-column tab-separated text file containing assembly
sequence names and sizes.
bosTau6.gc5Base.wigVarStep.gz - ascii data wiggle variable step values used
- to construct the GC Percent track
bosTau6.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
bosTau6.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
bosTau6.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/bosTau6/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/bosTau6/bigZips/ .
For a single file, e.g. chromFa.tar.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/bosTau6/bigZips/chromFa.tar.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/bosTau6/bigZips/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/bosTau6/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
Name Last modified Size Description
Parent Directory -
bosTau6.2bit 2011-05-10 09:12 668M
bosTau6.agp.gz 2011-06-14 09:01 1.8M
bosTau6.chrom.sizes 2011-05-09 12:09 65K
bosTau6.chromAlias.bb 2022-09-08 14:09 599K
bosTau6.chromAlias.txt 2022-09-08 14:09 84K
bosTau6.fa.gz 2011-06-14 09:15 828M
bosTau6.fa.masked.gz 2011-06-14 09:24 456M
bosTau6.fa.out.gz 2011-06-14 09:02 161M
bosTau6.gc5Base.wib 2019-01-17 14:45 508M
bosTau6.gc5Base.wig.gz 2019-01-17 14:45 10M
bosTau6.gc5Base.wigVarStep.gz 2011-05-09 12:16 1.3G
bosTau6.trf.bed.gz 2011-06-14 09:02 2.5M
est.fa.gz 2019-10-16 19:02 314M
est.fa.gz.md5 2019-10-16 19:02 44
genes/ 2020-02-05 13:46 -
md5sum.txt 2019-01-17 15:51 638
mrna.fa.gz 2019-10-16 18:45 11M
mrna.fa.gz.md5 2019-10-16 18:45 45
refMrna.fa.gz 2019-10-16 19:02 11M
refMrna.fa.gz.md5 2019-10-16 19:02 48
upstream1000.fa.gz 2019-10-16 19:03 3.5M
upstream1000.fa.gz.md5 2019-10-16 19:03 53
upstream2000.fa.gz 2019-10-16 19:03 6.7M
upstream2000.fa.gz.md5 2019-10-16 19:03 53
upstream5000.fa.gz 2019-10-16 19:03 16M
upstream5000.fa.gz.md5 2019-10-16 19:03 53
xenoMrna.fa.gz 2019-10-16 18:55 6.8G
xenoMrna.fa.gz.md5 2019-10-16 18:55 49
xenoRefMrna.fa.gz 2019-10-16 19:02 320M
xenoRefMrna.fa.gz.md5 2019-10-16 19:02 52