I am currently in the process of analyzing some RNA seq data from a mouse project and I was wondering if you are able to assist me with a small issue that I am having regarding whether or not to filter out non-relevant genes (e.g. immunoglobulin genes that may naturally be different between groups of mice) from my differentially expressed gene list.

Also, I was wondering if there is a way to remove false positive genes from a list of differential genes? For instance, some of the differential expressed genes are the same but belong to different regions or locus or a gene is showing up twice but with a different alias each time.