However i have another question:
I checked the OTU table and found the OTUs are low (with lots of zeros and lots of numbers below than 10) compared with the OTU table with same dataset generated by another software
I think the problem is from the filtering:
qiime taxa filter-table
–i-table unfiltered-table.qza
–i-taxonomy taxonomy-without-spaces.qza
–p-include 0__Bacteria
–o-filtered-table table.qza
My samples are about bacterial communities so i put O__Bacteria as a parameter to choose from.
There are so many reasons why you might be seeing different results - we would need to get some more details on what you did in QIIME 2 vs what you did in the other software.
Hmm, i'm not so sure about that --- filtering features removes entire features - it doesn't reduce the abundances within a given feature, though. It is an all-or-nothing kind of operation.
You are using a zero (0) in that prefix - is that correct? Also, what taxonomic database are you using? They all have subtle differences in how the taxon-labels are generated, so you won't necessarily be able to mix and match!
So, in order for us to help you out on this one, I think we need to learn more about what you did in this other software.
Your --p-include command you provided in your original post looks like it has a typo - you used the number zero instead of the letter O - can you confirm what you actually ran? That could cause some issues though, if you expected one but ran the other.
