I am new at this, and I am trying to clean CLIP data. I have a SE read results, that are supposed to have adaptors, and I am trying to figure out where these adaptors should be, on 5-prime end or 3-prime (or both?) RNA that had been PCRed using a specific illimina adaptor that adheres to 5', should they have left over adaptor sequences on the 5' end or the 3'? I read lots of posts but still can't wrap my head around the directions... Thanks!