Based on the Illumina note, am I correct in thinking that the same strand could be designated both “top” and “bottom” depending on which SNP was being examined?
You are correct in thinking that a long strand of DNA with many SNPs on it could have a different “top” or “bottom” designation at each SNP position based on Illumina’s top/bottom rule. Think of Illumina’s top/bottom strand designation as a strand rule in the “LOCAL” (to a SNP) sense. It is useful when comparing genotype data for each SNP, especially those SNPs with no (A/T, C/G) alleles. For an A/G SNP, if probe “A” produced a C/T result, and probe “B” produced an A/G result, then probe “A” is a bottom strand probe and probe “B” is a top strand probe. Notice that I said “probe ‘A ‘is a bottom strand probe” instead of “probe ‘A’ is ON the bottom strand”. To me, “ON” implies that a “top/bottom” designation applies to an arbitrarily long sequence, when in fact the “top/bottom” designation is just a way to compare each SNP genotype result. Again, the key phrase here is “LOCAL to a SNP”. Please use “orientation” flags to identify a sequence’s relative orientation to a contig, mRNA or genom
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