Get sequence by genomic coordinates in R
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!
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In R given a
BSgenome object, here
chr1:3000000-3000100, using the
my.dnastring <- as.character(Biostrings::getSeq(BSgenome.Mmusculus.UCSC.mm10, "chr1", 3000000, 3000100)) my.dnastring > NTTCTGTTTCTATTTTGTGGTTACTTTGAGGAGAGTTGGAATTAGGTCTTCTTTGAAGGTCTGGTAGAACTCTGCATTAAACCCATCTGGTCCTGGGCTTT
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