Low diversity and many non-classified sequences

Hi! I am starting working with microbiology and I am very newbie at this matter.

I am comparing a qiime1 pipeline with my new qiime2 pipeline.

When I compare sample1 with qiime 1 I can classify several different organisms. But in qiime2 I have 50% of my sequences classified at the the Domain level only.

I am suspecting I am training the classifier wrong?

qiime  tools import --type FeatureData[Sequence]  --input-path 99_otus_16S.fasta --output-path  99_otus_16S_silva.qza

qiime tools import --type 'FeatureData[Taxonomy]' --source-format HeaderlessTSVTaxonomyFormat --input-path consensus_taxonomy_7_levels.txt --output-path ref-taxonomy_silva.qza

qiime feature-classifier extract-reads --i-sequences 99_otus_16S_silva.qza --p-f-primer CCTACGGGRSGCAGCAG --p-r-primer ATTAGAWACCCBDGTAGTCC --p-trunc-len 300 --o-reads ref-seqs_silva.qza

qiime feature-classifier fit-classifier-naive-bayes --i-reference-reads ref-seqs_silva.qza --i-reference-taxonomy ref-taxonomy_silva.qza --o-classifier classifier_silva.qza

I would really appreciate some guidance solving this issue.


An off-topic reply has been merged into an existing topic: Low diversity… but maybe too low?

Please keep replies on-topic in the future.