Beta diversity on not normalised samples

[Nicholas_Bokulich]

Hi @llenzi,

@llenzi

Unfortunately, some of these come up with a number of sequences not far from samples

There can be many reasons for this: e.g., reagent contamination, cross contamination, and index jumping. There are lots of other discussions on the forum about how to handle negative controls and contaminants. Short story is it's a very open area of research, but these posts may be useful to you.

Now on to your problem:

@llenzi

Data must be symmetric and cannot contain NaNs.

I suspect you have one or more samples with zero reads. Since you are not doing any rarefaction, these will be retained (they are dropped automatically during single rarefaction).

You can use qiime feature-table filter-samples to drop any samples with 0 sequences (or better yet do a higher threshold).

@llenzi

(Also, any suggestion on how to deal with no so negative control samples?)

See the discussion link above. I suspect the majority of this is cross-contamination from real samples, in which case you cannot do something like drop all of the taxa observed in the negatives (in general that's a bad idea and one I do not recommend ever, if you read some of the other forum discussions).

I hope that helps!