@colinbrislawn .Thanks for your prompt response. This forum just has so many nice people. I will take your suggestion, to do the MSA on my DADA2 rep-seq. And in the meantime, i was inspired by this post Too many features? , so I will also try to do the downsteam analysis with or without filtering out the rare ASVs, see what could be the difference, and then decide which pipeline I am going to focus on; and also I will check other literatures on mice gut microbiota, to find out what is the feature table like in other studies, do these thoughts make sense to you? These are all the solutions I could come up with.
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