I have 3RAD data for studying SNPs. I'm quality-checking the reads, and found a very small quantity of adapter contamination, mainly Illumina universal adapter (FastQc says <0.1% (not even a warning), Process_radtags outputs 0.77% with 2 possible missmatches).
As I understand, I should not have, in theory, adapter contamiantion, as insert size is much longer than read length (around 550 bp vs 150bp). Should I still remove this small quantity of adapter sequences, assuming they are stranded small inserts that somehow passed size selection or should I just consider them false positives? What would be your usual approach to this situation?