STAR: the way to handle with multimapped read pair
Hello, everyone. I'm wondering how STAR handles with multimapped reads when using paired ends mode.
If one side of reads is a multimapper with the same score and the other is unique, how does STAR act?
I want to distinguish multimappers which have unique pair from multimappers whose pair is also multimapper.
Can STAR reflect mate pair status to FLAG, score, or any other information?
Thank you,
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