Thanks for your reply. Usearch and DADA2 used for generating OTUs and ASVs respectively from a dataset. These OTUs/ASVs were analysed by classify.seqs (MOTHUR) and assignTaxonomy(DADA2) using custom nifh and zehr nifh databases.
Custom and zehr databases compared in 4 combinations given below
- OTUs classified using MOTHUR (custom or zehr database)
- OTUs classified using DADA2 (custom or zehr)
- ASVs classified using MOTHUR (custom or zehr)
- ASVs classified using DADA2 (custom or zehr)
I understand variation within one of the 4 combinations that may be due to sequences in reference dataset (custom or zehr)
For example, the classification of OTUs using Custom database by DADA2 (No. 2) gives higher percent of classification and higher diversity compared to MOTHUR (No. 1). Here database is same, only platform is different. I would like to know the reason since dada and MOTHUR, both are based on naive Bayesian. I did not use MOTHUR for generating OTU.
Thanks and regards
Dinesh S L