Turning a Reference Genome Into a File With Single Nucleotide Positions (Essentially an ATCGmap.)
Hi all,
I am looking to turn a referenced genome into a file where every nucleotide is its own line. It'll be very similar to an ATCGMap file, except it won't have any methylation information. So column will be the chromosome, column 2 will be the nucleotide, and column 3 will be the position.
Anybody have any idea of the most productive way of going about this?
Thanks!
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What is the reasoning behind this task?
Hey,
I think I understand, but could you elaborate on the format of the referenced genome file?
The reference fasta is separated by chromosomes. Here's what I was thinking of doing: What I was planning on doing was to create a bed file based upon the chrosomes, and then expand the file for every single nucleotide. Only issue is I want to know what the reference genome nucleotide is at every position (almost like a VCF file or an ATCGMap file.)
You wanna tell us why?