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?
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?
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Jennifer Jackson http://usegalaxy.org/ http://galaxyproject.org/
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?
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- 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@mac.com
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?
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- 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@mac.com <mailto:edwardturk@mac.com>
-- Jennifer Jackson http://usegalaxy.org/ http://galaxyproject.org/
participants (2)
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Edward Turk -
Jennifer Jackson