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  • #16
    Simon,

    Thanks. The "--samout" option works great. I can see each read with its assignment to a feature with the tag ‘XF’. My next question is how do I extract reads with no_feature, ambiguous, and alignment_not_unique from the rest of the mapped reads?

    Thanks.

    Tilahun

    Comment


    • #17
      Originally posted by abebe View Post
      Simon,

      Thanks. The "--samout" option works great. I can see each read with its assignment to a feature with the tag ‘XF’. My next question is how do I extract reads with no_feature, ambiguous, and alignment_not_unique from the rest of the mapped reads?

      Thanks.

      Tilahun
      Just use grep.

      Comment


      • #18
        dpryan and Simon,

        Thanks for your help. A combination of samout and grep solved my questions.

        Keep up the good work.

        Cheers.

        Tilahun

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