I am trying to run explore if there are any differences between taxonomy between two clinical groups (weight gain and weight loss). I read the songbird tutorial on github but not sure I fully understand what to write for the command as it’s not working.
I’m using QIIME2-2020.2
This is the command I’m writing (please see my questions after the ## for each of the lines):
qiime songbird multinomial \ --i-table filtered-allpaired.qza \ (### *that is my feature table after I filtered low abundance features)* --m-metadata-file metadata.tsv \ *(## can my metadata contain blanks for the WeightChangeCategory column or do I need to filter in advance)* --p-formula "Wt_chng_category" \ (*### As I said, I'm tying to explore whether taxons differ between the two weight change cateogries. Is that where I enter this variable)* --p-epochs 10000 \ (*## do I change this number?Not sure I really understand what this represents?? I know that this number means how long I need to run Songbird, but again not sure I grasp the meaning for this)* --p-differential-prior 0.5 \ *(### again not sure I know what that means and if I need to change it?)* --p-summary-interval 1 \ (### again not sure I know what that means and if I need to change it?) --p-training-column Training \ --o-differentials differentials.qza \ --o-regression-stats regression-stats.qza \ --o-regression-biplot regression-biplot.qza
Thank you so much in advance!