Question: BBmap : how to output only unique alignment
1
gravatar for Nicolas Rosewick
2.7 years ago by
Belgium, Brussels
Nicolas Rosewick7.6k wrote:

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 
                        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.

Thanks

Edit : I solved the problem by putting ambiguous=toss

bbmap • 1.1k views
ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by Nicolas Rosewick7.6k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1104 users visited in the last hour