Hi developer,
Can I merge the bacterial profiling file and virus profiling file together ? Or just output all results (including bacteria and virus) to one file ?
Thanks!
Hi @fujch7
Unfortunately it is not possible to merge the outputs because for viruses we only report depth and breadth of coverage, while for the other microbes we report the relative abundance, so they are not directly comparable. The reason is that in MetaPhlAn we use markers to estimate the abundance of microbes, but for phages we use the full genome. This is because for viruses it is very difficult to define viral genomic markers that work due to the high diversity and mosaicity of their genome and therefore we consider a phage to be present if reads map against more than 75% of the phagic genome, but we can’t really estimate the abundance from this information.
There will soon be an update in the code to include at least an estimation of reads assigned to the virus (e.g. RPKM) and full taxonomy for each reported virus.