Hi,
I am a beginner in the Qiime2 language. I am writing with two goals.
First, I try to use the new version of Greengenes. Can you revise
my code? My imports are 2022.10.backbone.full-length.fna.qza and 2022.10.backbone.tax.qza.
I read on another post that these files are correct to use the most recent version...
4.1.1
qiime feature-classifier extract-reads
--i-sequences metadata/2022.10.backbone.full-length.fna.qza
--p-f-primer CCTACGGGNGGCWGCAG
--p-r-primer GACTACHVGGGTATCTAATCC
--p-trunc-len 0
--p-min-length 100
--p-max-length 480
--o-reads training-feature-classifiers/greengenes_ref-classif-seqs.qza
--p-n-jobs 8
qiime feature-classifier fit-classifier-naive-bayes
--i-reference-reads training-feature-classifiers/greengenes_ref-classif-seqs.qza
--i-reference-taxonomy metadata/2022.10.backbone.tax.qza
--o-classifier training-feature-classifiers/greengenes_classifier.qza
qiime feature-classifier classify-sklearn
--i-classifier training-feature-classifiers/greengenes_classifier.qza
--i-reads training-feature-classifiers/greengenes_ref-classif-seqs.qza
--o-classification training-feature-classifiers/greengenes_taxonomy.qza \
qiime metadata tabulate
--m-input-file training-feature-classifiers/greengenes_taxonomy.qza
--o-visualization training-feature-classifiers/greengenes_taxonomy.qzv
4.1.2
qiime feature-classifier classify-sklearn
--i-classifier training-feature-classifiers/greengenes_classifier.qza
--i-reads DADA2/rep-seqs-hits90.qza
--o-classification training-feature-classifiers/taxonomy_greengenes_myseqs.qza
--p-n-jobs 8
qiime metadata tabulate
--m-input-file training-feature-classifiers/taxonomy_greengenes_myseqs.qza
--o-visualization training-feature-classifiers/taxonomy_greengenes_myseqs.qzv
qiime taxa barplot
--i-table DADA2/final-table-hits90.qza
--i-taxonomy training-feature-classifiers/taxonomy_greengenes_myseqs.qza
--m-metadata-file metadata/micro_metadata_def.tsv
--o-visualization training-feature-classifiers/taxa-bar-plots_taxonomy_greengenes.qzv
Second, I have a big doubt when I have to extract results. I have many results such as:
|k__Bacteria| p__Bacteroidetes| c__Bacteroidia| o__Bacteroidales| f__[Paraprevotellaceae]| g__[Prevotella]| s__|0.9934940329633781|
|k__Bacteria| p__Bacteroidetes| c__Bacteroidia| o__Bacteroidales| f__Prevotellaceae| g__Prevotella| s__|0.9999016163134539|
|k__Bacteria| p__Bacteroidetes| c__Bacteroidia| o__Bacteroidales| f__Prevotellaceae| g__Prevotella| s__stercorea|0.999999678905164|
Why any family results are ? And why can the classifier classify the same genus for different families?
I think that this output can be uncorrected...
Can anyone help me, please?