I’m looking to normalize paired RNA and DNA abundances from meta-samples analyzed with Humann3.
The Humann3 wiki suggests:
For low-abundance species, random sampling may lead to detection of transcripts for undetected genes. In these cases, we recommend smoothing DNA-level features to avoid divide-by-zero errors during normalization.
Are there commands/options to do this smoothing in Humann3, or do I perform this on my own? Perhaps it’s automatically done in the CPM normalization step? When I searched for this I couldn’t find it in the Humann2/3 wikis or tutorials, but I did see that Humann (legacy) included a Witten–Bell smoothed output file.