Hi Patrick:
I am using mothur to deal with my 16s data. I amplified v3 and V6 region and sequenced them with 250bp pair-end reads. After align.seq, align report told that most of the SearchScore is under 100 by kmer methods, does that matters? Thanks a lot.


The best possible search score is 100 so I wouldn’t worry about things being below 100. Although you want a high number there, we find that align.seqs does very well even with distantly related sequences. You might also keep in mind that the V6 region is a very difficult region to work with because it is so variable.


Thanks a lot,Pat. I’ve tried to analyze V3 and V6 regions by mothur. When using align.seqs, search scores in V6 were lower than V3. And more unclassified OTUs in V6 than V3 at genus level. So in the following study, I will choose V3 region. Thanks AG.


Why not just use V4?

Sometimes our sequencing core generate not very good data. Usually I need to trim 50bp at the 3’end. So I want to try v3, even trim 50bps each reads, I still can get full covered sequence of V3 by 250PE.

If you’re going to go away from V4, I’d suggest checking this out…