Qiime2 version: 2019.1
After running the qiime taxa barplot command, and visualizing the results through the output .qzv file, there appears to be a potential error when collapsing abundances by different levels of taxonomy. The error seems to be related to when there is missing or unclear taxonomy at a higher level and trying to collapse to a lower level of taxonomy.
For example, I am looking to visualize and understand genera level differences within my samples but have two bars associated with unknown genus from the family Lachnospiraceae. One entry is:
While the other entry is:
The difference here seems to be the presence or absence of a “g” when you have an unknown entry.
As the greengenes database I am using for the taxonomic assignments does not have any taxonomic entries without an identifier, I’m wondering if this is a result of parsing within the command.
The code used for the analysis is here:
!qiime feature-classifier classify-sklearn
!qiime metadata tabulate
!qiime taxa barplot
Please let me know if you have any possible explanations for this.