downloading a reference genome: Saccharomyces_cerevisiae_S288C_SGD2010
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/S2...), 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
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/S2...), 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,
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Douda Bensasson -
Jennifer Jackson