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Old 07-06-2010, 07:39 AM   #2
BENM
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Location: PRC

Join Date: May 2009
Posts: 33
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I think you'd better to run sampe for each PE files separately:

bwa sampe [options] <prefix> <in1.sai> <in2.sai> <in1.fq> <in2.fq>

Although you concatenate all read files into two PE seq is okay, I recommend you split them (for example: 100M reads per files) and run in different CPU cores or computer nodes (MPI mode), so that it would be more faster.
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