[galaxy-user] Yeast Genome Assembly

[Jennifer Jackson]

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
> edwardturk at mac.com <mailto:edwardturk at mac.com>
>
>
>
>
>
>

-- 
Jennifer Jackson
http://usegalaxy.org/
http://galaxyproject.org/