Can I conclude anything from MiSeq primer reads?

Question

[francois]

I am sequencing with MiSeq loci I targeted with CRISPR-Cas9. I sometimes have many paired small primer reads (see pic attached), Can I conclude anything from them? They are definitely not random, I see more often at specific loci/in some samples. Can they be hint of large deletions?

Answer 1

[Friederike]

Primer dimers are an indication that the library prep could be optimized; there's either an abundance of primers (or scarcity of PCR-able fragments of interest) or too many PCR cycles or all of it.

I don't think it would be appropriate to use them as evidence for anything related to your actual question of interest because they are quite frequently occurring artifacts.

Answer 2

[swbarnes2]

Primer dimers don't tell you anything.