Hello,
Given a chromsome and single-base position for a species, I need to retrieve the called base in the reference genome. I'm looking for an existing way with R/Bioconductor for this.
I am looking at the bioconductor package rtracklayer, which I know can already retrieve existing annotations (e.g. UCSC) in R-readable format. For now, I have been able to retrieve start and end of transcript and CDS for genes associated with genomic positions, but not single nucleotides at a specific position.
Otherwise, I'm thinking about reading and retrieving the reference base called directly from the reference genome in fasta (.fa) format.
Any already existing easy method would be appreciated, however.
Given a chromsome and single-base position for a species, I need to retrieve the called base in the reference genome. I'm looking for an existing way with R/Bioconductor for this.
I am looking at the bioconductor package rtracklayer, which I know can already retrieve existing annotations (e.g. UCSC) in R-readable format. For now, I have been able to retrieve start and end of transcript and CDS for genes associated with genomic positions, but not single nucleotides at a specific position.
Otherwise, I'm thinking about reading and retrieving the reference base called directly from the reference genome in fasta (.fa) format.
Any already existing easy method would be appreciated, however.
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