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Old 01-24-2018, 06:03 AM   #204
milan.molbio
Junior Member
 
Location: Switzerland

Join Date: Jan 2018
Posts: 3
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@sdriscoll thanks for the tip! with these two options bbmap does report one 100% semiperfect site read but it's not in the output file. Anything else I'm missing?

the exact command was:
Code:
bbmap.sh secondary=t sssr=0.80  k=3 maxindel=0 strictmaxindel  ref=sample.genome.fa ambiguous=all   maxsites=10  in=sample.read.fa out=mapped.sam vslow
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