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  • why the properly paired results from bwa mem is an odd number

    Hi
    following is the results of samtools flagstat results. I use bwa mem default command to do align! my question is why the properly paired is odd number?

    25700926 mapped

    25744459 + paired in sequencing

    12897523 read1

    12846936 read2

    25445603 properly paired

    25692729 with itself and mate mapped

    8197 singletons

    my reads are from a archaea RNA-seq experiment.

    and how to get unique mapped read-pairs from the properly paired?

    thanks!

  • #2
    That is because of chimeric alignment.

    Comment


    • #3
      Thanks for your reply!

      Comment

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