I’ve created the following artifacts via the following methods:
OTU abundances .tsv file --> biom --> FeatureTable[Frequency]
taxonomy .tsv file --> FeatureData[Taxonomy]
tree .nwk file --> Phylogeny[Rooted]
Now that I’ve converted all of the data to artifacts, is there a method directly available in qiime for checking that the sample/feature IDs imported correctly and all of the IDs overlap between the artifacts? Given that at least for some qiime commands, there’s no warning if sample/feature IDs don’t overlap (samples/features are just silently filtered), I want to make sure all of my artifacts match. In R, one could do this with the
intersect() functions, but I don’t see anything equivalent in qiime2. Am I missing it?
System versions Python version: 3.5.4 QIIME 2 release: 2017.10 QIIME 2 version: 2017.10.0 q2cli version: 2017.10.0 Installed plugins alignment 2017.10.0 composition 2017.10.0 dada2 2017.10.0 deblur 2017.10.0 demux 2017.10.0 diversity 2017.10.0 emperor 2017.10.0 feature-classifier 2017.10.0 feature-table 2017.10.0 gneiss 2017.10.0 longitudinal 2017.10.0 metadata 2017.10.0 phylogeny 2017.10.0 quality-control 2017.10.0 quality-filter 2017.10.0 sample-classifier 2017.10.0 taxa 2017.10.0 types 2017.10.0 vsearch 2017.10.0