Redoing analysis from QIIME 1, Archaea has mostly disappeared

[SoilRotifer (Mike Robeson)]

@Emily_Sprague

OK, to confirm, I'm currently waiting on the following command to finished running:

@Emily_Sprague

Then I will use this classifier output with classify-sklearn, correct? If this gives me the taxonomy I was expecting, I can just use the data as-is at that point, right? I wouldn't have to go back and try something different with extract-reads?

Correct. On occasion an amplicon specific classifier can improve classification. Though this depends on how the reference data is curated. But is quite optional. You can change-up the order on how to prepare your database too.

For example, if you only want to make an amplicon-region specific classifier with RESCRIPt, you can run the following:

1. qiime rescript get-silva-data ...
2. qiime rescript reverse-transcribe ...
3. qiime rescript dereplicate ... Optional derep of full-length seqs. You can skip to next step, 4 .
4. qiime feature-classifier extract-reads ... extract region using your primers
   • Optionally supplement with qiime extract-seq-seqments ... to extract amplicons that are missing primer sequence.
5. qiime rescript dereplicate ... Derep extracted seqs. Seqs might be identical over the region extracted
6. qiime rescript cull-seqs ... Optional, but highly recommended.
7. qiime rescript filter-seqs-length-by-taxon ... or qiime rescript filter-seqs-length ... Optional.
8. qiime feature-classifier fit-classifier-naive-bayes ...