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Question: Get sequence by genomic coordinates in R
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gravatar for a11msp
4 months ago by
a11msp • 110
European Union
a11msp • 110 wrote:

I've realised that after many years of using R, I still don't know a good way to extract a sequence by genomic coordinates. I tried using bioMart, but it seems like getSequence() can't just get any sequence, it asks for some anchors such as gene name, etc. Would appreciate your advice!

sequence R • 263 views
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modified 4 months ago by ATpoint ♦ 44k • written 4 months ago by a11msp • 110
6
gravatar for ATpoint
4 months ago by
ATpoint ♦ 44k
ATpoint ♦ 44k wrote:

In R given a BSgenome object, here chr1:3000000-3000100, using the Biostrings library:

my.dnastring <- as.character(Biostrings::getSeq(BSgenome.Mmusculus.UCSC.mm10, "chr1", 3000000, 3000100))

my.dnastring
> NTTCTGTTTCTATTTTGTGGTTACTTTGAGGAGAGTTGGAATTAGGTCTTCTTTGAAGGTCTGGTAGAACTCTGCATTAAACCCATCTGGTCCTGGGCTTT
ADD COMMENT • link modified 4 months ago • written 4 months ago by ATpoint ♦ 44k

This is great - thanks very much!

ADD REPLY • link written 4 months ago by a11msp • 110
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