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  • Novoalign Output Missing

    Hi,
    I have run novoalign in multiple ways, but each time when the program finishes running, I cannot find the output file! -o just specifies the output format. There are no errors during the run. Can you tell me where the alignment file is or how I could find it?
    Thank you!

  • #2
    ./novoalign -o SAM -d [file.novoindex] -f [read_1] [read_3] 1> [output.sam] 2> [output.metrics]

    That should be a basic way to run it.

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    • #3
      That worked perfectly. THANK YOU!!

      Comment


      • #4
        Hi guys!

        Just resurrecting this thread - had exactly the same problem as the OP, but now it works.

        Just what exactly are the output.metrics?

        Comment


        • #5
          Like the number of reads, number of aligned etc.

          Originally posted by TabeaK View Post
          Hi guys!

          Just resurrecting this thread - had exactly the same problem as the OP, but now it works.

          Just what exactly are the output.metrics?

          Comment

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