Dear all,
I am trying to understand when rarefaction is appropriate. My samples were sequenced to the same target depth, but the number of reads retained after processing—and the number of ASVs—can still differ among samples. Some differences in ASV richness may reflect the sampling environment. Should I rarefy the data before comparing alpha diversity? I am concerned that discarding reads could change the results.
I have also noticed differences in reported Shannon diversity values for what appears to be the same data. When I calculate the index in R with vegan, I get different values from those reported elsewhere. Could this be due to the choice of logarithm base? My understanding is that vegan uses the natural logarithm by default. How should the base be reported so that results can be compared?
I would appreciate any guidance on both points. Thank you in advance!