increased total sequences following trim.seqs

Hi there,

I currently have v.1.39.5 installed. I have a 16s dataset that was previously processed within mothur v.1.33.3, which I just ran again using the same pipeline, but with my current mothur version. One of the major differences I’ve noticed is that following trim.seqs for the same dataset, mothur v.1.33.3 obtained:

unique: 520,462

total: 2,854,782

whereas mothur version 1.39.5 obtained:

#unique: 851,096
total: 5,020,634

I’ve looked over the various updates that have occurred since v. 1.33.3, but I just can’t seem to pinpoint what change would result in nearly twice as many total sequences making it through the trimming stage. Any thoughts here? Thanks in advance!!

Are you using pdiffs or bdiffs? Mothur now reports the diffs separately for paired primers.

Thanks for the reply!

I used bdiffs=0, pdiffs=2 in both instances.