I'm stuck with where to place the bisulfite treatment control for pyrosequencing. For forward sequencing (where sequencing primer binds lower strand) I have identified potential positions where a C is not followed by a G and therefore should be converted to T if bisulfite treatment successful. But how do I know whether to add the control before or after?
Also, what is different if I have reverse sequencing? Is it a G not after C should be a T? And does the control go before or after in this instance?
Hope someone can help!