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 database Saccharomyces_cerevisiae_S288C_SGD2010 could be
an update (newer release) of the SGD/sacCer2 database, since the
is the same - SGD:
UCSC did not update to this newer version of the genome (yet), which
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
UCSC. But using the latest genome from SGD would give you the highest
quality assembly to work with and viewing in Trackster
at Galaxy is a great alternative.
Hopefully this helps,