Are they the same?-"taxonomy.qza" from alignment and phylogeny building and " taxonomy_rep-seqs.qza" fromTaxonomy classification and taxonomic analyses


Hi, I am new to qiime2, currently I am trying to use qiime2 to do taxonomy analysis for my 16S sequence data.
I used two methods respectively from the instruction of qiime2 overview flow chart,
After join, quality control and de-noise with deblur for my sequences, I go through the steps in section " Sequence alignment and phylogeny building" as following,
qiime fragment-insertion sepp \
--i-representative-sequences rep-seqs_D35.qza \
--o-tree insertion-tree.qza \
--o-placements insertion-placements.qza


qiime fragment-insertion filter-features \
--i-table table_D35.qza \
--i-tree insertion-tree.qza \
--o-filtered-table filtered_table_D35.qza \
--o-removed-table removed_table_D35.qza


fragment-insertion classify-otus-experimental \
--i-representative-sequences rep-seqs_D35.qza \
--i-tree insertion-tree.qza \
--o-classification taxonomy.qza


Then I go through steps in section " Taxonomy classification and taxonomic analyses" as following:
qiime feature-classifier classify-sklearn \
--i-classifier ../reference/gg_13_8_otus/classifier.qza \
--i-reads Clean_Data_D35_joined_filtered_rep-seqs.qza \
--o-classification taxonomy_Clean_Data_D35_joined_filtered_rep-seqs.qza


metadata tabulate \
--m-input-file taxonomy_Clean_Data_D35_joined_filtered_rep-seqs.qza \
--o-visualization taxonomy_Clean_Data_D35_joined_filtered_rep-seqs.qzv


my question are the taxonomy results from both sections the same?, i.e is "taxonomy.qza" the same as "taxonomy_Clean_Data_D35_joined_filtered_rep-seqs.qza"?(looks they are very similar!)
If they are the same, that means two sections are just different methods for taxonomy assignment?
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Good morning zong,

Welcome to the forums! :qiime2:

Yes! They both include a taxonomy classification table for each of your features.

That’s correct! Note that fragment-insertion classify-otus-experimental is experimental, just like it says in the name, so you might want to use an established classification method for publication.

Colin

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@colinbrislawn Thank you very much, Colin!