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Old 06-02-2013, 03:44 PM   #4
shi
Wei Shi
 
Location: Australia

Join Date: Feb 2010
Posts: 235
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Dear Jon Keats,

The distance is measured as the distance between the mapping location of the leftmost base of the left read and the mapping location of the leftmost base of the right read. So for your example, the distance between the two reads is 49 (50-1).

We will make the usage info more clearer for these two arguments.

Best wishes,

Wei
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