[BioC] BSgenome package for sacCer3
Hervé Pagès
hpages at fhcrc.org
Thu Oct 13 02:58:27 CEST 2011
Hi,
This is to announce that a BSgenome package for sacCer3 is now available
in BioC devel (i.e. R 2.14 + BioC 2.9):
> library(BSgenome.Scerevisiae.UCSC.sacCer2)
> sacCer2 <- Scerevisiae
> library(BSgenome.Scerevisiae.UCSC.sacCer3)
> sacCer3 <- Scerevisiae
> seqlengths(sacCer2)
chrI chrII chrIII chrIV chrV chrVI chrVII chrVIII chrIX
chrX
230208 813178 316617 1531919 576869 270148 1090947 562643 439885
745742
chrXI chrXII chrXIII chrXIV chrXV chrXVI chrM 2micron
666454 1078175 924429 784333 1091289 948062 85779 6318
> seqlengths(sacCer3)
chrI chrII chrIII chrIV chrV chrVI chrVII chrVIII chrIX
chrX
230218 813184 316620 1531933 576874 270161 1090940 562643 439888
745751
chrXI chrXII chrXIII chrXIV chrXV chrXVI chrM
666816 1078177 924431 784333 1091291 948066 85779
The 2micron sequence is gone.
The package is only available as a source package for now. Binaries
for Windows and Mac will follow soon. In the mean time, users on those
platforms should be able to install from source (i.e. with
biocLite(..., type="source")).
Announcement by UCSC:
https://lists.soe.ucsc.edu/pipermail/genome-announce/2011-October/000233.html
Starting page for browsing this new assembly:
http://genome.ucsc.edu/cgi-bin/hgGateway?clade=other&org=S.+cerevisiae
Cheers,
H.
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpages at fhcrc.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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