Hi,
I have used silva 132 qiime release to learn training on 16s V3-V4 region ( I know there is a post in the forum provided the classifier but I am doing this for learning purpose).
Testing the classifier of silva 132 qiime release on 16s V3-V4 region yielded only Taxons belonging to Archae result.
which seems odd, I would expect bacteria taxons come out from it.
For input sequences, I used <rep set 16s only> at 99; for taxonomy, I used <16s only><99> consensus_taxonomy_7_levels.txt
Workflow:
printf "Import Sequence\n"
qiime tools import
--type 'FeatureData[Sequence]'
--input-path ../silva_132_99_16S.fna
--output-path silva_132_99_16S.qza
printf "Import taxonomy file\n"
qiime tools import \
--type 'FeatureData[Taxonomy]' \
--input-format HeaderlessTSVTaxonomyFormat \
--input-path ../consensus_taxonomy_7_levels.txt \
--output-path taxa_silva_ref_16s.qza
printf "Extract reference reads\n"
qiime feature-classifier extract-reads \
--i-sequences silva_132_99_16S.qza \
--p-f-primer CCTACGGGNGGCWGCAG \
--p-r-primer GACTACHVGGGTATCTAATCC \
--p-trunc-len 500 \
--o-reads ref_silva_16s_99_seqs.qza
printf "Train the classifier\n"
qiime feature-classifier fit-classifier-naive-bayes \
--i-reference-reads ref_silva_16s_99_seqs.qza \
--i-reference-taxonomy taxa_silva_ref_16s.qza \
--o-classifier classifier_silva_16s_99.qza
qiime feature-classifier classify-sklearn \
--i-classifier classifier_silva_16s_99.qza \
--i-reads ref_silva_16s_99_seqs.qza \
--o-classification taxa_test_training.qza \
--n-jobs 1 \
--p-reads-per-batch 1000
qiime metadata tabulate \
--m-input-file taxa_test_training.qza \
--o-visualization taxa_test_training.qzv
I think I either used the wrong files or missed some steps?
Thanks.