Before LEfSe analysis..

Hello guys

I got a taxonomy data and now i want to proceed LEfSe analysis.

I want to know what data usually use to input file.

Are you using the raw sequence count obtained as a result of taxonomy? Or do you use data converted to ratio (%, relative abundance)?

Overall ratio of the control group and the treatment group should be compared, so the ratio is correct, right?

I am a newbie in microbiome analysis, please help me!

If I am not mistaken, you are right and Lefse requires relative abundances as an input.

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Thanks :slight_smile: . I appreciate your quick reply !