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  • Brian Bushnell
    Super Moderator
    • Jan 2014
    • 2709

    #16
    Maybe you are including secondary alignments. What was your command for mapping?

    Comment

    • mmmm
      Senior Member
      • Jul 2013
      • 131

      #17
      n50 or nodes

      bwa mem -t 4

      Comment

      • Brian Bushnell
        Super Moderator
        • Jan 2014
        • 2709

        #18
        bwa mem will produce multiple primary mappings per read, so the statistics won't be comparable between assemblies. You can use -M to mark these as secondary.

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