Question- Do I have to subsample before running MetaPhlAn3?

Microbial community profiling MetaPhlAn
1

Hello, so I am new to this and was wondering if I have to subsample before running MetaPhlAn3?

From what I understand I do not have to subsample before running HumanN3 as it has a built-in utility script (humann_renorm_table) either “relab” (relative abundance) or “cpm” (copies per million).

I would like to run MetaPhlAn3 and plot a graph comparing the taxonomic profile between different groups.

Many thanks

2

Hi, you don’t need to subsample your metagenomes if their size is comparable, in case you have a big difference in size (around one order of magnitude), I would consider subsampling.

There are also recent threads on this topic, I’ll leave here the links in case you want to have a look (#283 and #320)