I ran into problems with merging OTU table and taxonomy names after filtering.
I filtered out mitochondria and chloroplast using the following code:
qiime taxa filter-table --i-table table.qza --i-taxonomy taxonomy.qza --p-mode exact --p-exclude ‘k__Bacteria; p__Cyanobacteria; c__Chloroplast; o__Streptophyta; f__; g__; s__’ --o-filtered-table table-filtered2.qza
qiime taxa filter-table --i-table table-filtered2.qza --i-taxonomy taxonomy.qza --p-mode exact --p-exclude ‘k__Bacteria; p__Proteobacteria; c__Alphaproteobacteria; o__Rickettsiales; f__mitochondria’ --o-filtered-table table-filtered.qza
after filtering, the exported OTU table have 4769 lines while the exported taxonomy table have 4806 lines. Because of the uneven length of OTU table and Taxonomy table, I had problems in merging them together. (The unfiltered tables does not have this issue, OTU table and taxonomy table have the same feature ID from up to down).
I tried to use
qiime taxa collapse --i-table table.qza --i-taxonomy taxonomy.qza --p-level 3 --o-visualization feature-table-class.qza
it returned error message “Collapse groups of features that have the same taxonomic assignment through the specified level. The frequencies of all features will be summed when they are collapsed.” The error message does not make sense to me because my level 3 taxonomy are different, not the same as the error message suggested.
Does anyone know how to solve this issue?