Using balance-taxonomy on collapsed taxa

[biotama]

Continuing the discussion from Gneiss on collapsed FeatureTable:

Hi,
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?

Thanks

[mortonjt (Jamie Morton)]

Hi @biotama, have you tried out the qiime taxa collapse command? That can be found in the moving pictures tutorial: https://docs.qiime2.org/2018.8/tutorials/moving-pictures/#differential-abundance-testing-with-ancom

[biotama]

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
--i-table lastcompositiondeux.qza
--i-tree lasthierarchydeux.qza
--i-taxonomy taxonomydeux.qza
--p-taxa-level 5
--p-balance-name 'y0'
--m-metadata-file metadatavrgeneiss.tsv
--m-metadata-category samplingperiod
--o-visualization lastyz_taxa_summaryzq-fivelevelp.qzv
error: None of [..........] are in the [index]"

Here is my code after creating taxonomy table which mutch with qiime2-collapsed table

qiime tools import
--input-path table.biom
--output-path taxonomyb.qza
--source-format BIOMV210Format
--type "FeatureData[Taxonomy]"

Error:biom.exception.TableException: Duplicate observation IDs
and here is my "home collapsed taxonomy table"
mergetax.txt (58.0 KB)

thanks for helping

[mortonjt (Jamie Morton)]

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.

Gneiss on collapsed FeatureTable

Hi @mortonjt, Collapsing beforehand would merge many singletons features into the same taxon labels thus eliminating the need to exclude them before running Gneiss. However, I still filter any remaining singletons features from the collapsed table afterwards. If the balance-taxonomy collapses internally why sometimes the same taxon can be found in both the numerator and denominator? Best, Ali