Hi Edward,
We will add the new yeast genome from Feb 2011 to our working list of
genomes to add. (r64 dated Feb-3-2011 at SGD, dated April 2011 at NCBI).
This confirmed with SGD directly to be a more current version that the
two currently at Galaxy. The S288C_reference_genome_r64.tar.gz download
is here:
http://downloads.yeastgenome.org/genome_release/r64/
Meanwhile, the data can be loaded and added to your history and used
from there as a reference genome with most tools.
Best wishes for your project!
Jen
Galaxy team
On 6/29/11 2:22 PM, Edward Turk wrote:
Hi Jen,
Could you update the yeast genome to match the following 2011 release?
Ensembl release 9 for Fungal database (which is dependant on SGD
database) [link :
http://fungi.ensembl.org/Saccharomyces_cerevisiae/Info/Index].
Thank you,
Edward
On Jun 27, 2011, at 11:58 AM, Jennifer Jackson wrote:
Hello Edward,
The database Saccharomyces_cerevisiae_S288C_SGD2010 could be
considered an update (newer release) of the SGD/sacCer2 database,
since the source is the same - SGD:
http://www.yeastgenome.org/
UCSC did not update to this newer version of the genome (yet), which
is why in Galaxy it is not labeled with a UCSC short name (for
example, sacCer3). If/when UCSC decides to create a sacCer3 genome
database, we would very likely pull that over or add in the short name
to the existing Galaxy genome (if they were the same build).
There are advantage with deciding to use either. If using the UCSC
genome, liftOver would be available as well as the option of viewing
at UCSC. But using the latest genome from SGD would give you the
highest quality assembly to work with and viewing in Trackster
(Visualization at Galaxy is a great alternative.
Hopefully this helps,
Jen
Galaxy team
On 6/24/11 8:40 AM, Edward Turk wrote:
For yeast analysis I use the following assembly: S. cerevisiae June
2008 (SGD/sacCer2) (sacCer2). Recently a new yeast genome has
appeared as an option in Galaxy: S. cerevisae str. S288C
(Saccharomyces_cerevisiae_S288C_SGD2010). Is this an update to
sacCer2? Where is it coming from? I don't see it at UCSC?
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--
Jennifer Jackson
http://usegalaxy.org/
http://galaxyproject.org/
Dr. Edward Turk, Ph.D.
Postdoctoral Fellow
Dep. of Molecular Biology and Microbiology
Case Western Reserve University
School of Medicine, Wood Bldg. W212
10900 Euclid Avenue
Cleveland, OH 44106
440-487-2928
216-368-0385
edwardt...@mac.com mailto:edwardt...@mac.com
--
Jennifer Jackson
http://usegalaxy.org/
http://galaxyproject.org/
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