Hi Fabiola,
Sorry for the delaying. I used these steps below. As stated in the tutorial, I by skip this step
- Extract reference reads
qiime feature-classifier extract-reads … --o-reads ref-seqs.qza
Because the ITS sequences do not need the extraction or trimming, it should be used on the full reference sequences.
Please find below the steps for training.
qiime tools import
–type ‘FeatureData[Sequence]’
–input-path sh_refs_qiime_ver7_dynamic_01.12.2017.fasta \ (the fasta file containing the sequences)
–output-path shrefsdyn.qza
qiime tools import
–type ‘FeatureData[Taxonomy]’
–input-format HeaderlessTSVTaxonomyFormat
–input-path sh_taxonomy_qiime_ver7_dynamic_01.12.2017.txt \ (the txt file containing the taxonomy Kingdom………Species)
–output-path ITS1ref-taxonomy.qza
Making the classifier file
qiime feature-classifier fit-classifier-naive-bayes
–i-reference-reads shrefsdyn.qza
–i-reference-taxonomy ITS1ref-taxonomy.qza
–o-classifier ITSclassifier.qza (The classifer file to be used in step 13)