<p>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.</p>

CC BY-SA 4.0
2020-01-07T13:39:04.447Z
2020-01-07T13:39:04.447Z
Wouter De Coster
<p>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?</p>

<p>Thanks</p>

<ngs><adapter><cutadapt><fastqc>
Why don't all reads have adaptors?
# Why don't all reads have adaptors?

(Asked by: username_0 on 2020-01-07)

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?

Thanks

**Tags:** ngs, adapter, cutadapt, fastqc

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## 1 answers

### Answer by username_1 on 2020-01-07. Score: 8 | Accepted answer

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.


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