I used two different nifh databases individually (zehr and fungene) as well as in combined form for classification using MOTHUR. I am getting higher percentage of classification for certain genera, for example 37 reads were classified as Sideroxydans using fungene but only one was classified when combined with Zehr database. I would like to know the reason for disparity.
The cutoff used for all three classifications were 89. Thanks
I don’t know much about these two databases, but based on what we’ve seen with 16S classification, I suspect the two databases vary in the sequences represented in them and the taxa they include.