Removing genes manually before RNA-seq normalization is not a good practice, right? For example, we would like to investigate osteoblast expression from bone samples, but we know that there is some contamination from muscle. Is it correct to remove the 'muscle' genes before normalization? I understand this should not be done because TMM normalization corrects for library size and compositional biases. Imagine that some bone samples are more contaminated than others, and one has an extremely high expression of muscle genes. If we compare two different conditions and remove the contaminating transcripts before normalization, we would obtain untrustful results, right?
Another example would be removing all non-coding genes beforehand if we want to study protein-coding genes, only. The same applies?