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Old 09-19-2013, 11:30 PM   #3
Curious Character
Location: Berlin, Germany

Join Date: Sep 2010
Posts: 13


Make sure the BAM file is sorted by coordinate and the splitted alignment is defined by N cigar code (true for tophat by default).

Also you might check some alternative ways to calculate coverage, for example using coverageBed and intersection with annotation file:
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