I have come across examples of people filtering out immunoglobulin genes during RNA-seq analysis, such as in this paper :
However, I am interested in the immunology of the condition I am studying and hence in the expression of these genes.
Is there a reason why they should be removed?
If yes should these genes, alongside non-coding genes, pseudogenes etc. be filtered before or after normalisation & differential expression analysis with Deseq?
Thank you for the thoughts.