Chromosome position to nucleotide - Biostrings?
1
3
Entering edit mode
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
ADD COMMENT
2
Entering edit mode
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
ADD COMMENT

Login before adding your answer.

Traffic: 479 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6