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?
Good morning zong,
Welcome to the forums!
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
@colinbrislawn Thank you very much, Colin!
Hi Colin, what does experimental mean? based on the wet lab experiment or based on some experiment census?
Another question regarding phylogenic tree building, I am doing chicken gut microbiota analysis,
which approach I should choose, "reference-based [fragment insertion] approach"? or "
de novo approach"? what is the criteria for making decision for phylogenic tree building approach?
Zong
Here, I think "experimental" means "unconventional" or "prototype" or "work in progress". The fragment-insertion
plugin includes validated methods like sepp, it also includes this new, experimental method for classifying otus.
(Once the new method has been validated, it will probably be called classify-otus
)
Good question! There is evidence that reference-based [fragment insertion] approach works better than denovo tree building (especially for short reads). There is a good example of using sepp in this part of the Parkinson’s Mouse Tutorial.
Colin
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