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Old 04-29-2013, 08:46 PM   #1
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Location: NYC

Join Date: Feb 2013
Posts: 7
Default Typical alignment mapping percentage with genome?

What are typical mapping percentages for alignment? My samples are giving me an average of approx. 25% mapping coverage (from pair end 100bp reads). STAR produces somewhat fewer mappings than Tophat, but that's not surprising.

What kind of mapping numbers are you seeing? What do you expect? To what do you attribute the numbers, and how do you interpret them?

Thanks in advance.
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