[khmer] option -p for SE and PE reads

C. Titus Brown ctb at msu.edu
Wed Oct 9 18:45:43 PDT 2013

On Thu, Oct 10, 2013 at 09:39:46AM +0800, cy_jiang wrote:
> Hi all,
> I got both PE and SE reads after adapter trimming and quality control. Now that I want to diginorm both of these reads. I noticed that there is an option -p used for PE reads during the normalization. I wonder what may happen if I first combine the SE to PE reads and the use -p for diginorm. Hope to hear from soon and many thanks in advance!
> Best regards,
> Daniel

Hi Daniel,

The -p flag will crash if the reads aren't all paired.  See


for some instructions on dealing with this.

C. Titus Brown, ctb at msu.edu

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