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BENM · 07-06-2010, 08:39 AM

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.

07-06-2010, 08:39 AM	#2
BENM Member Location: PRC Join Date: May 2009 Posts: 33	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.