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
## F: 5'-CCTACGGGRSGCAGCAG-3'
#R: 5'-GGACTACHVGGGTWTCTAAT-3'
#rev-comp Rl: ATTAGAWACCCBDGTAGTCC
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.
thanks!