I want to use balance taxonomy from gneiss as the last step to identify taxa that are different depending on some conditions but I have the same issue and I am wondering how to collapse the taxonomy.qza in order to much with the collapsed table and do the analysis?
Hi mortonjt, thanks for reply
Yes this was what I did but actually this function collapse only the feature table and not the taxonomy table which results in a not mutching between two tables (as discussed previously in this forum)
while to run the balance-taxonomy we need the taxonomy table also, so my question is there anyway to collapse the taxonomy table in the same way as feature table?
PS:when collapsing feature table, we loose the feature IDs, I tried to merge the two tables in R and import the taxonomy table into .qza and I got error
This what I did at the first time
qiime gneiss balance-taxonomy
error: None of [..........] are in the [index]"
Here is my code after creating taxonomy table which mutch with qiime2-collapsed table
HI @biotama, it is also worthwhile pointing that if you collapse your biom table, the balance-taxonomy command is not expected to work with this format due to the taxonomy. I am not aware of a collapse taxonomy command just for the taxonomy.
(Matthew Ryan Dillon)