I am analyzing a time series of a metatranscriptome. In metatranscriptomics, we have to do the regular normalizations found in RNA-Seq (ie. gene sequence length, and sample-differences in total expression). However, there is an additional normalization required to account for changes in species abundance.
I would like to analyze differences in species-level transcript abundance, so I've done all these normalizations. But to then analyze differential expression with DeSeq2, it seems I shouldn't put the normalized values as input. Is there a recommended way around this?
Any tips or advice is appreciated!