Hi,
 

How can I find the nucleotides, given the chromosome and the genomic positions? I was trying to use the Biostrings package, but couldn't find the function that would give me the nucleotides. For example, how do I find the nucleotides at the following positions on Chr15 (homo sapiens):

67494484,67494485,67494486,67494489,67494490,67494504

Is there any other package that would be more convenient?

thanks!

Use the getSeq method of the Biostrings package.  It works with multiple representations of reference genomes, and accepts GRanges as inputs.

library(BSgenome.Hsapiens.UCSC.hg19) ## our reference sequence
library(GenomicRanges) ## GRanges lives here

gr = GRanges("chr15", IRanges(67494484, width = 1))

getSeq(BSgenome.Hsapiens.UCSC.hg19, gr) ## yields the sequence 'A' at this position