I’m pretty sure there would be a way to do this but I can’t seem to find how. Ultimately would look at both rare and abundant datasets separately.
I don’t think there is an option for percentages with split.abund (unless I missed it).
Alternatively to use split.abund, I think that filter.shared might do a better/faster job (as can directly use a shared file) using makerare=F but I’m not sure if there is a way to output the rare/removed OTUs (e.g. as an accnos-type file or “rare.shared” file). Same problem with remove.rare, not sure if there is a way to access the removed OTUs.
Any suggestions, work around?
Worst case was thinking of subsampling a list and fasta file in order to have the same number of sequences in all groups and then using split.abund with a cut-off that would match my desired percentage cut-off but would not be ideal.
Thanks a lot (you guys are great!)