I use bbmap to align paired-end reads and would like to know if this parameter is the right one to change in order to report only uniquely mapped reads :
maxsites2=800 Don't analyze (or print) more than this many alignments per read.
But when I put maxite2=1 it gives me an error :
BBMap version 36.27 Exception in thread "main" java.lang.AssertionError: maxsites2 must be at least 2.
Could someone help me to understand this parameter ? and to output only the uniquely mapped reads.
Edit : I solved the problem by putting ambiguous=toss