I have 30 samples (3 replicates * 10 conditions) running Miseq experiment to evaluate library quality. fastqc reported 2 (from the same condition) out of 30 have high sequence duplication levels (obviously outliners). I went back to check RNA quality and read abundance in those two samples, nothing weird. After mapping those two to reference transcriptome, no difference on alignment percentage from others.
Then what make those two libraries specially high sequence duplication? Should I re-make library before proceed to Hiseq?