I am using Bowtie 2 version 2.1.0 for pair end RNAseq reads mapping to the CDS(Protein coding gene sequences). I am not able to understand the default setting of mismatch in Bowtie2.
I can see there are two option related to mismatch:
--mp : max penalty for mismatch;lower qual = lower penalty (6)
-N : mismatches in seed alignment; can be 0 or 1 (0)
Please suggest what is the difference between these two and how I can adjust mismatch during mapping.
My aim is to map pair-end read to reference CDS (protein coding gene sequences) and to do raw read count.