Hello everyone,
I’ve received a set of alpha diversity data from a collaborator and I’m unsure about which specific data I should use for the analysis of the Shannon diversity index. The table includes different columns with values for "sequences per sample" and "iteration" across several rarefaction levels. Additionally, I have calculated values for other alpha indices, such as Chao1 and observed_species.
My main question is: which value of sequences per sample and iteration would be most appropriate to generate boxplots representing Shannon alpha diversity?
I would appreciate any guidance on whether I should use a specific iteration or if there is a recommended number of samples per sequencing for this kind of analysis.
Thanks in advance for your help!
