The Pair Specifier dialog lets you choose the method for recognizing paired reads.

To access the dialog, use Project > Project Parameters. If the Pair Specifier section is not already active, click on Pair Specifier on the left.

  • Choose from typical pair naming conventions in the Pair Pattern drop-down menu.

    If you choose Custom, you will need to enter the custom naming convention in the Forward and Reverse boxes.
  • Under Paired-End Insert, enter integers for the Minimum and Maximum expected distance (in bp) between the forward and reverse paired reads.

Click OK.

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