View Single Post
Old 07-06-2010, 08:39 AM   #2
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.
BENM is offline   Reply With Quote