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Old 09-16-2009, 12:32 AM   #2
Simon Andrews
Location: Babraham Inst, Cambridge, UK

Join Date: May 2009
Posts: 870

It's certainly possible. Most paired end mapping algorithms are able to use mapping information about one end to infer a likely position for the other, meaning that a read which in isolation couldn't be mapped uniquely can be positioned if the position of its other end is known.

If you see a big difference in efficiency I'd also double check that you were using the same mapping parameters in both runs just to be sure. Using 75bp reads I'd be surprised if there was a big advantage to using paired end over single end mapping for a cDNA library.
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