FastQC is not recognising that there are adaptors

Question

[Miss]

FastQC is not recognising that there are still adaptors before trimming. Do you think it is because I have merged many files together?

[jared.andrews07]

That shouldn't matter. And by merging "files", I assume you mean concatenating FASTQs from the same sample that was sequenced across lanes?

How do you know there are adaptors? FastQC presumably only checks for the most common adapters, so if you have a less common platform/setup, then perhaps it wouldn't recognize them.