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Old 06-11-2012, 05:57 PM   #2
ECO
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Location: SF Bay Area, CA, USA

Join Date: Oct 2007
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Read up on paired end or mate-pair libraries.

The short answer is, by mapping reads derived from both ends of a molecule, one can "size" that molecule against the reference genome. If you know you made your library with 250bp physical molecules, and the ends of that molecule map 10kb apart in the reference genome, you can infer that your sample genome has a deletion.
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