Hi @f.asnicar
MetaPhlAn3 has detected 84% microbacterium phage in one of my samples but the same result is not found by other taxonomic profiling programmes. Also, none of the other samples is showing this much viral diversity that too only a single Phage which is microbacterium phage. How is that possible?
I need a proper explanation of this issue. I had already enquired about it previously but did not get respond. Please help!
Hi,
The virus profiles obtained with --add_viruses are to take it with a grain of salt since the method was kept as experimental from MetaPhlAn2. 84% is a relative abundance, not an absolute abundance. It is possible that the hits identified as viral are over-represented in the total number of mapped reads, which I suppose are very few.
ok, so shall I do the analysis again with all the samples since I had added this --add_viruses flag with all my datasets? Because I think in all the profiles I am getting over-representation of viruses as relative abundances of viruses is around (15-25)% in all the samples. What would be your advice?
Yes, I would also have a look at the relative abundances obtained with --unknown_estimation in order to see how many reads are mapping against each clade.