Chromosome position to nucleotide - Biostrings?
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Brian Smith ▴ 120
@brian-smith-6197
Last seen 4.2 years ago
United States

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!

biostrings • 2.0k views
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Julian Gehring ★ 1.3k
@julian-gehring-5818
Last seen 5.6 years ago

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
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