Hello List,

I am trying to retrieve a sequence of ~1000 nts using the getseq() function
from the BSgenomes package

I would like to replace the repeat masked regions with Ns

using something similar to the inject snps function from the
SNPlocs.Hsapiens.dbSNP package.

So far I can grab sequence from the genome either masked: getSeq(Hsapiens,
"chr21",  33665196, 33665435,  as.character=FALSE)

or unmasked: getSeq(hg19snp, "chr21",  33665196, 33665435,
as.character=FALSE)

The problem is that the masked function returns a gap:

TCCCAGGATGTGACATTGTTTGCCAGTGCAGAGGC...GGAGCTTTGGAAGAAGAGAGAGTTGACTACGGAAA

 and I would like the gap to be filled with Ns?

Thanks in advance,

Pete

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