Hello:
I ran my Illumina 2x150bp 10 million reads samples in Metaphlan 4.0.6 insede Biobakery workflows with mpa_vOct22_CHOCOPhlAnSGB_202212 database. Then I build a phyloseq object in R and try to plot relative abundance in a ggplot with phyloseq aggregated to Species (microbiomeutilities::aggregate_top_taxa2) and compositional transformation (phyloseq::transform_sample_counts). I obtained up to 75% of Unknown relative abundance.
When I analyzed the same samples in a Metaphlan3 2 years ago I did not obtained any Unknown.
Is that Unknown percetage normal?
Thank you