Hello Douda,
This genome is sourced from build R64 (not R63), the
"NCBI_genome_source" version, with some modifications made to the
chromosome identifiers. The original data is available from SGD and NCBI
(April 2011 http://www.ncbi.nlm.nih.gov/assembly/285498/).
The chromosome identifiers between the sources can vary, but the
chromosome sequences are identical. Galaxy used identifiers like: "chr1,
chr2, ... chrM".
The genome is mislabeled and we will be correcting. However, if you
would like to obtain the current version as on Galaxy Main before the
change is made, the genome can be obtained from our rsync server.
Instructions are in this post:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-July/010607.html
Very sorry for the confusion this may have caused,
Jen
Galaxy team
On 8/8/12 1:16 PM, Douda Bensasson wrote:
We have mapped our ABI SOLiD reads to the "Yeast (Saccharomyces cerevisiae) str.
S288C: Saccharomyces_cerevisiae_S288C_SGD2010" reference in Galaxy, and need to
compare our yeast genomes to the reference.
We have tried to download the only S. cerevisiae S288c genome release listed at SGD for
2010 among their genome releases
(http://downloads.yeastgenome.org/sequence/S288C_reference/genome_releases/S288C_reference_genome_R63-1-1_20100105.tgz),
but this does not align with the consensus sequences generated by mapping against
Galaxy's "Saccharomyces_cerevisiae_S288C_SGD2010".
Is Galaxy's Saccharomyces_cerevisiae_S288C_SGD2010 reference available for
download from Galaxy or from the Saccharomyces Genome Database (SGD)?
Best wishes,
Douda
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___________________________________________________________
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
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use the Galaxy Development list:
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