Hi, I want to try using
qiime vsearch uchime-ref on my ASVs that I've obtained after running Deblur. This is because I've noticed there are still a lot of chimeras in my dataset. On a side note -- has anyone else had this issue with chimeras and Deblur, and what did you do about it?
Anyway, the developer of usearch recommends trying both -mode high_confidence and -mode balanced in this case. I am wondering what the equivalent parameters are for
qiime vsearch uchime-ref? I suspect it is setting the value of
--pminh, but not sure what I should set that to for this case ( mode high_confidence having a high false negative rate and mode balanced trying to balance false pos and negative).
I'd appreciate any insight, thanks!