clarification/verification of taxonomy classifiers

[SoilRotifer (Mike Robeson)]

@Rob_DNA

Alright so these files - see 2 files selected in grey in the picture below to make sure we are talking about the same files - are not actually the ''raw'' files, but have first been processed by RESCRIPt to make them more QIIME-compatible (as is stated on the page).

Correct. We made use of the processing steps as outlined in the tutorial.

@Rob_DNA

You mention that RESCRIPt can be used for own curation of the SILVA database etc. However, for "general usage" (how one would define this)

This is explained, in detail, through the RESCRIPt SILVA tutorial I linked in my initial response.

@Rob_DNA

the 2 files I use are suitable for creating a trained classifier based on extracted reads using own primers, right?

This would be the quickest way to proceed, as much of the general processing has been performed for you. In effect, you would be continuing from this step of the tutorial.

Again, if you do not agree with the processing steps outlined in the tutorial you can start from scratch and process as you'd like. Also, I think the pre-made files are using SILVA 138 and not the updated 138.1 version. This is now the default version in RESCRIPt, i.e. rescript get-silva-data ... .