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Is CHG methylation strand-symmetric? #72

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PeteHaitch opened this issue May 15, 2014 · 1 comment

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PeteHaitch commented May 15, 2014

Should --strandSpecific be required if methylationType CHG is provided?

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PeteHaitch commented May 20, 2014

No. Specifically, a CCG is not strand-symmetric (because the complement of H is D).

Strand	Sequence	methylationType
-	GTC	CHG
+	CAG	CHG

-	GGC	CG
+	CCG	CHG, CG

-	GAC	CHG
+	CTG	CHG

Therefore, is possible for a CHG to exist on one strand but not the other.

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