I have read many manuals of alignment tools, many of them deal the multiple mapped by reporting the best alignment base on their alignment score (such as bowtie,BWA), but i want to know if i already set the mismatch as zero, then all multiple mapped should be same score right? What can i do to avoid reads that can find multiple perfectly matches?
What do you mean exactly?
i can understand if mapping with allowing some mismatches there will be different in alignment score, but if i don't allow any mismatch it should be all perfectly match and same score.