Does lefse takes care of rare taxa or feature?

Downstream analysis and statistics LEfSe
1

Hi… I have unstratified output from HUMAnN 3.0. I want to find out differentially abundant pathways between two groups. For that, I have removed those features (pathways) which are not present in at least 10% of the total samples. But, in addition, should I also need to remove those features which show relative abundance below a certain percentage in any sample? I just want to know if there is any additional filtering step needed or not.

Thanks,
DC7

2

Hi,

Filtering for prevalence and abundance is always a good idea to avoid spurious hits.

Best,
Kelsey

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