I have 2 questions that i am trying to solve for quite some time now, hopefully you could help me
** im using qiime2 11.18 version **
Im working on fungi ITS2 region, my pipe line is based on this amazing ITS2 tutorial : Q2-ITSxpress: A tutorial on a QIIME 2 plugin to trim ITS sequences
- I am trying to understand how qiime2 transforms my features from dada2 to taxonomy labels using the taxa plugin. For example, when im testing my mock community i get 36 features in the taxonomy.qzv but my taxa-bar-plot.qzv gets only 25 taxonomy labels. i tried to read about this in the forum and taxa doc, but im not sure i fully understand the “collapsing” process. I also tried to cluster the features to OTUs using 2 (de-novo | Open ref) different methods in this tutorial: https://docs.qiime2.org/2019.1/tutorials/otu-clustering/
To try to get the same results as in the taxa-bar-plots. i got identical results in the csv files.
but my feature table shrinked from 36 to 31 (when i tried 99% OTU ) or to 29 (97% OTU).
So i would love to know how it works!
my pipeline taxonomy qzv: taxonomyDevee5_Trim6.qzv (1.2 MB)
my pipeline taxa-bar plots qzv: taxa-bar-plotsDEV_EE5_Trim6.qzv (336.8 KB)
99% OTU clustering: taxonomy_OpenRef_99%.qzv (1.2 MB)
97% OTU clustering : taxonomy_OpenRef_97%.qzv (1.2 MB)
- The second questions is bit more tricky, but i think it might help others as well.
When i used the dada2 in the denoising step i raised the MAX error rate to 5 (default 2) because i was losing 30-50% of my reads and now i lose only 5-10%. i just wanted to know that this is “legal” and i can continue with my analysis.