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  • Star alignments and samtools flagstat

    I ran some paired-end RNAseq alignments using STAR (default options) and then I ran samtools flagstat on the sorted bam files I always get
    '0 + 0 duplicates'

    All the other stats from flagstat appears consistent but I cant imagine with several million PE reads I get no duplicates.

    Any Ideas

  • #2
    Hi David,

    Flagstat just counts the SAM flags, so if you haven't marked reads as duplicates (generally through a tool such as picard MarkDuplicates), then you won't see any.

    Whether or not you want to mark/remove duplicates in RNA-seq is another matter. I think for many RNA-seq applications, such as differential expression with high depths, it is not desirable to do so.

    Comment


    • #3
      Thanks a lot for your help.

      Cheers

      Dave

      Comment

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