SILVA 16S database

[SoilRotifer (Mike Robeson)]

Hi @AndreaC, welcome to !

@AndreaC

I get completely different percentages

Couple of questions:

1. Do you know if that working group trained their classifier specific to the V3 region? This could be a potential reason for any differences observed.
2. I assume they classified the same dataset as you are currently working with?
3. Which QIIME 2 sequence identification tool did they use for classification? That is, did they use the nàive bayes classifier, vsearch, blast?

@AndreaC

while from the "Silva 138 99% OTUs database from 515F / 806R region of sequences "I don't get any classification.

The reason why you are seeing lack of classification on your V3 16S rRNA amplicon region, is due to the fact that the Silva (515F / 806R) is specific to the V4 region, which does not overlap at all with your V3 data.

@AndreaC

I have seen that the SILVA database can be downloaded and customized with RESCRIPt, however I do not have enough RAM to perform the operation.

Great to hear that you are trying RESCRIPt! If you have been dereplicating the data, especially after extracting your amplicon region of interest, you should not need too much RAM. How much RAM do you have?