I’m currently running some metatranscriptomic data (without accompanying metagenomic data) through Humann2.
The study design is quite simple, disease state vs. healthy controls, and I would like to find out what taxons are differentially abundant (I understand that abundance is to be taken with a grain of salt in this case due to the nature of single copy marker genes), which gene families/pathways are differentially expressed, and look at any associations between taxonomy/function and clinical metadata.
My question is whether MaAsLin2 and LEfSe are suitable for statistical analysis on the Humann2 functional outputs for this type of data? I would normally use DESeq2 for RNA-Seq data if I was aligning to reference genome(s) but I do not think it would be suitable here as I will not have raw count data.
Any advice would be greatly appreciated,
All the best,