I apologize if this subject was already discussed.
I prepared my small RNA library using NEXTflex Small RNA-seq kit, which has 4 randomized nucleotides at the ends of both adaptors (to reduce ligation bias). After looking at my alignments, I am pretty sure that some of my IP samples contain plenty of PCR duplicates. I am trying to figure out a way to use the randomized adaptors ends as UMIs. Is it OK to do it this way? Could I get a recommendation for a tool to do it?