Dear officer,
I have a question regarding FUGAsseM Coexpression-based input file preparation. I’ve read the tutorial and have two questions about the input file preparation.
My first question concerns the MTX abundances table for protein families in each sample. I understand that I can use HUMAnN to generate a normalized GO format protein list for each sample, and I should skip the nucleotide-level pangenome mapping during this process. Is that correct? Once I obtain the normalized protein list from each sample, should I then calculate the total protein abundance for each bacterium in every sample? Is that correct?
My second question relates to the GO gene-cluster list. Is this list meant to identify which bacteria possess specific GO proteins (i.e., excluding proteins with 0 abundance for each bacterium)?
Best wishes,
Shuyuan