I would like to ask if it possible to run the subsampling command for couple of times, not just once. It been suggested to me to make sure that I got all the sequences after running this command, instead of getting rid of the important sequence that i could get.
Can you please clarify to me this point if is it possible and why in case of no ?
You can rarefy the data in summary.single and dist.seqs by using subsample=T or subsample=### where ### is the number of sequences you want. This will subsample 100 or 1000 times and then give the average. The sub.sample command can be run multiple times on a shared file, but it will write over the results each time. This is really only appropriate when you’re investigating the associations for individual OTUs.