BBmap : how to output only unique alignment
0
1
Entering edit mode
5.7 years ago

Hi,

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


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.

Thanks

Edit : I solved the problem by putting ambiguous=toss

bbmap • 2.0k views