http://seqanswers.com/forums/showthread.php?t=10
Detection of a true SNP is reflected by changes in two adjacent colorspace calls, which must follow the rules above. Figure 7 below gives some examples of this principle in examining alignments.
If you’re doing the math you’ve realized there are 16 possible dinucleotides (4^2) and only 4 dyes. So data from a single color call does not tell you what base is at a given position. This is where the brilliance (and potential confusion) comes about with regard to SOLiD. There are 4 oligos for every dye, meaning there are four dinucleotides that are encoded by each dye.
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