REANALYSING DATASET IN DADA2- Taxa assign

[Ka-di1]

Hi! I am reanalyzing a gut microbiome dataset that was originally processed with UPARSE. However, I encountered an issue with taxonomy assignment in DADA2.

Initially, I used standardized filtering parameters:
truncLen = c(240,160), maxEE = c(2,2),
but this resulted in very few taxa being assigned. To improve classification, I adjusted the filtering parameters to:
truncLen = c(250,190), maxEE = c(2,5), which yielded around 17 genera.

I tested both RDP and different SILVA versions, and I also reattempted assignment using tryRC=TRUE. However, the results still do not align with the original study, which confirmed certain species using qPCR.

Would you have any insights on why the taxonomy assignment might be underperforming compared to the original? Could this be due to differences in read processing, database compatibility, or another factor?

Thanks in advance for your help!