how to set up max mismatches be 15 via bwa

[shuang]

I have an RNA-seq dataset of average 100 nt long. I need to generate an alignment and output in sam format.

I'm using bwa. I want to set up the number of maximum mismatches of a read alignment to be 15. How to I set up parameters to fit my goal? Or any other tools could do the trick?

[nilshomer]

15 mismatches would be a 15% error rate. That would take a very long time to perform a breadth first search with BWA. You may want to try other mapping strategies that could have more sensitivity with that level of dissimilarity.