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HUMAnN2 input to LEfSe

Hello,
I want to compare pathway abundances generated using HUMAnN2, by LEfSe.
I merged tables across samples, and performed humann2_split_table, and now I have a raw table, a stratified table, and an unstratified table.

From my understanding, I should input a raw table to LEfSe, as in the MetaPhlAn2 tutorial they input a table which preserves the rank (not summarizing to a certain rank). However, I saw some websites and papers that input an unstratified table.

What input is desirable to perform differential analysis? Is it depending on the purpose of analysis?

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