Question: BBmap : how to output only unique alignment
gravatar for Nicolas Rosewick
3.6 years ago by
Belgium, Brussels
Nicolas Rosewick8.7k wrote:


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

bbmap • 1.4k views
ADD COMMENTlink modified 3.6 years ago • written 3.6 years ago by Nicolas Rosewick8.7k
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