I downloaded the 16S V4 region of some species of Fusobacterium. Then I made it a taxonomy classifier to identify the specific species of Fusobacterium in my samples. And I’m wondering if it is appropriate to do so and what is the default similarity for sequence alignment in Qiime2.
Welcome to the forum, @qw4521099!
Depends what taxonomy classifier you use. This would be inappropriate if you are using the naive Bayes classifier (classify-sklearn), since you are feeding in limited amount of information you would make a very weak classifier that could misclassify non-Fusobacterium species. You could use these Fusobacterium reference sequences with
classify-consensus-vsearch, however, setting higher thresholds for percent identity and coverage to make sure that sequences are only classified if are very similar to Fusobacterium.
Depends what method you use! You can check the help docs for any method to learn more — e.g.,
qiime feature-classifier classify-consensus-vsearch --help will give you all the answers you need for that method.
Thank you so much. You’ve helped me a lot. I didn’t expect that my post would be replied.