I have a question regarding duplication levels shown in MultiQC report. The raw data went through HTStream for preprocessing and MultiQC was used to check. In the report I saw that when I ran multiQC on 3 different lanes of the same sample it had about 40% duplication for all three lanes (L001, L002, L003 had 40-41%) but the same sample had about 60% duplication when all 3 lanes were combined. Can anyone explain the reason for this?
Any help is appreciated! Thank you.