Dear List,

I am creating a TranscriptDatabase as follows:

library(GenomicFeatures)
myDB <- makeTranscriptDbFromBiomart(biomart = "ensembl", dataset = "scerevisiae_gene_ensembl", circ_seqs = c(DEFAULT_CIRC_SEQS, "Mito"))
myDBx <- cdsBy(myDB, by = "tx", use.names = TRUE)

everything fine so far,
I am just missing 4 ORFs which are present on the 2 micron plasmid. (R0010W, R0020C, R0030W, R0040C)


If one puts here http://www.yeastgenome.org/cgi-bin/seqTools "R0010W",
one finds the following info:
FLP1/R0010W, ORF, on 2-micron plasmid from coordinates 252 to 1523.


While the annotation from Ensembl is imported from SGD, no ORFs are listed for the 2-micron plasmid, and therefore
also not accessible via makeTranscriptDbFromBiomart.

Any hints what I am getting wrong?

Best,
Stefanie
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