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Old 06-23-2011, 01:51 PM   #5
Location: Bay Area

Join Date: Jan 2009
Posts: 58

Any idea why BWA needs reads to be inner directional (---> <---) for it to map them.

I guess Tophat will not work as the read lengths are variable and as per my understanding of the version I used they require read 1/2 of equal length. In our case based on the identification of linker the read length will be variable.

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