Relative abundance interpretation

[cliffbueno]

Hello,
Thanks for a great tool. I wanted to clarify the relative abundance interpretation from mTAGs, specifically with regard to dealing with unaligned and unassigned counts. You stated "The two last rows represent all sequences that could not be aligned or that could be aligned but could not be assigned at this taxonomic level. For almost all downstream analyses, it is better to remove this value, since it does not represent a single taxa but it needs to be taken into account when computing relative abundances."

So, in the example, would you conclude that Basidiomycota has relative abundance of 0.70 (1310/1859)? Or could you argue that the unaligned and unassigned sequences are "junk" and shouldn't be counted? I ask because in 16S PCR amplicon studies, we usually remove reads that are unassigned at the domain level. In this case the relative abundance of Basidiomycota would then be 0.95 (1310/1385).
root__Root;domain__Archaea;phylum__Euryarchaeota 1
root__Root;domain__Bacteria;phylum__Actinobacteriota 2
root__Root;domain__Bacteria;phylum__Firmicutes 1
root__Root;domain__Bacteria;phylum__Proteobacteria 5
root__Root;domain__Eukaryota;phylum__Apicomplexa 1
root__Root;domain__Eukaryota;phylum__Ascomycota 57
root__Root;domain__Eukaryota;phylum__Basidiomycota 1310
root__Root;domain__Eukaryota;phylum__Phragmoplastophyta 1
root__Root;domain__Eukaryota;phylum__uncultured 1
root__Root;domain__Eukaryota;phylum__unknown 6
Unaligned 427
Unassigned 47

Thanks,
Cliff