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Old 05-08-2010, 11:13 AM   #2
Location: Berkeley, cA

Join Date: Feb 2010
Posts: 40

The correct way to deal with reads that map to multiple places is explained in the paper by Li et al:

Mathematically, the ambiguity that arises from multiple hits in alignment, is no different than the ambiguity that arises when reads can belong to multiple isoforms at one location- in fact the statistical deconvolution is identical.

We plan to extend Cufflinks to correctly solve this problem in the near future.
Currently, multiple hits are assigned equal probabilities- details are in the supplement to the Cufflinks paper:
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