taxonomic profile from rarefied OTU tables?

[camillaln]

Hi,
Is it possible to make a taxonomic profile from rarefied OTU-tables?
Thanks,
Camilla

[wwood]

Hi,

Good question. Not directly - the rarefication only outputs TSV OTU tables, which aren't enough info to make taxonomic profiles.

Implementing is possible, but as a workaround you could run pipe to get an archive OTU table, and then summarise --unaligned-sequences-dump-file to get the raw sequences picked up by pipe, rarefy those sequences yourself, and then put those through pipe -p to get a condensed profile.

Make sense? Complicated stuff, I'm afraid, though possible.

[camillaln]

Thanks! I will try :)
Camilla