Hello,

First of all, thank you so much for developing qiime2 and other plugins, which are very helpful for my research. I would like to ask your help with the differential abundance analysis.

I used Songbird and Qurro for processing differential abundance analysis of 16S sequencing data of 5 environmental samples with 3 different treatments (15 samples in total).

It seems to be fine for the fit of my model. This is my command.

qiime songbird multinomial

–i-table filter-table-2nd.qza

–m-metadata-file sample-metadata.tsv

–p-formula “C(Source, Treatment(‘sludge’))”

–p-epochs 100000

–p-differential-prior 0.1

–p-summary-interval 0.1

–p-random-seed 3

–o-differentials Source-differentials.qza

–o-regression-stats Source-regression-stats.qza

–o-regression-biplot Source-regression-biplot.qza

–verbose

qiime songbird multinomial

–i-table filter-table-2nd.qza

–m-metadata-file sample-metadata.tsv

–p-formula “1”

–p-epochs 100000

–p-differential-prior 0.1

–p-summary-interval 0.1

–p-random-seed 3

–o-differentials filtered-null-diff.qza

–o-regression-stats filtered-null-stats.qza

–o-regression-biplot filtered-null-biplot.qza

qiime songbird summarize-paired

–i-regression-stats Source-regression-stats.qza

–i-baseline-stats filtered-null-stats.qza

–o-visualization Source-paired-summary.qzv

But visualization of the differential rank using Qurro shows only 5 OTUs were used to set up the model. Do you know the reasons for this result?

This is my command

qiime qurro differential-plot

–i-ranks Source-differentials.qza

–i-table table.qza

–m-sample-metadata-file sample-metadata.tsv

–verbose

–o-visualization Source-qurro_plot.qzv

Thank you for spending your time.

Best regards,

Pham