I generated some paired end data using simNGS and simLibrary, as they seem to be very good for illumina HiSeq.
My problem is that novoalign does not recognize the pairs, and returns "No pairs found". It is strange because when mapping my real illumina data, it performs excellently. Any suggestions would be very helpful.
Before suggestions to use different mappers are made, I already tried BWA (which worked fine) and Stampy (same problem as novoalign). Are there known issues with simNGS and mapper compatibility?
My problem is that novoalign does not recognize the pairs, and returns "No pairs found". It is strange because when mapping my real illumina data, it performs excellently. Any suggestions would be very helpful.
Before suggestions to use different mappers are made, I already tried BWA (which worked fine) and Stampy (same problem as novoalign). Are there known issues with simNGS and mapper compatibility?
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