Thank you in advance for your help! I am pretty new to this analysis. I have run my samples through metaphlan3 for a microbiome analysis and am quite happy with the output relative abundance tables. How do I move forward to calculate my alpha and beta diversity? Can this be done in metaphlan3?
I am also trying to normalize my data so I can normalize resistance genes. Is there a way I can observe what the average length of alignment was to the database? And, would I be able to observe the number of alignments to the bacteria sequence per sample?
Thank you so much!