I got NGS reads back from sequencing platform. I check for adaptors and trimmed them. But I realized only a fraction (eg 30%) have adaptors... why not all of them?
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Things like this might depend on your specific library prep, but in general: sequencing starts at the end of the adapter, not before it. You will only see adapters if you sequence through the entire fragment into the adapters on the other side. If your fragment is long enough you won't see any adapter, and of course, that's the desirable outcome of your library prep.