Dear All,
While QIIME2 has great statistical feature for alpha and beta diversity, which were not present in QIIME1.
I am curious if we can have the same for taxonomy. I wish I could have 2 things in taxonomy analysis.
taxonomy Bar plots per group and not per sample. Currently in moving picture tutorial command qiime taxa barplot
gives only per samples barplot.
I wish we could have mean/median per group for each bacterial feature plus ANOVA/ Kruskal-Wallis test p value for each bacteria.
Hi @drmusk both of these things exist and are described in the documentation.
Use qiime feature-table group to group your samples before making a barplot.
See ANCOM (in q2-composition). ANOVA and kruskal-wallis tests are NOT appropriate for microbiome data (relative abundance data breaks assumptions of independence and normality).
Thanks for helping out. It worked.
I am doing analysis for more than 1 experiments. For my second experiment, I used qiime feature classifier to get taxonomy.qza
I am using Qiime2core2018.11 and therefore used previously downloaded gg-13-8-99-515-806-nb-classifier.qza file with Qiime2core2018-11.
Using the next 2 commands I got taxonomy.qzv and taxa-bar-plots.qzv
Surprisingly, in taxonomy.qzv and taxa-bar-plots.qzv I get only level 1 classification.
Kingdom Bacteria, Unknown. No phyla, class or other things. taxa-bar-plots.qzv (316.2 KB)
Please help. I am guessing that with QIIME2Core2018-11 qiime feature-classifier classify-sklearn didn't work well.
No, this is not an issue related to the classifier itself or with the version of QIIME 2 that you are running. When only kingdom level classification is achieved, it is a user error: you are using a classifier that is inappropriate for your data (e.g., wrong type of data or targeting the wrong site). This issue has been discussed several times on the forum, and I encourage you to search the archives on this topic for more advice on troubleshooting.
