Average after multiple rarefaction in QIIME whitout alpha-diversity

[Irelka Colina]

Hello!

I want to know if someone know a command to use after multiple rarefaction and make an average of new files (100 files) whitout making alpha-diversity.

I used this command, but I do not found something to continue,

multiple_rarefactions.py -i otu_table.biom -m 12612 -x 12612 -s 10 -n 100 -o rarefied_otu_tables/

I used some commands in "R", but I do not if is possible to do directly sur QIIME,

Thanks, 
Irelka

[justink]

Hi Irelka, I don't think there is a way to make such an 'average of rarefied tables'. I think we've mostly felt that it leads to confusing results (what if you have .01 sequences of OTU1? and if you round up, don't you put back some of the oversampling bias you removed when you performed rarefaction in the first place?).

Of course, we can't think of everything. If you do average the tables, keep in mind that many beta diversity measures assume integer counts of each OTU.

Best!

Justin