Human vs Mouse - Homologues

Question

[andrebolerbarros]

Hey everyone,

I have some RNASeq data and an unconventional analysis to perform: I have samples from Human and Mouse, and I want to perform DEG between these two sets.

Now, I thought about two ways to go for this:

• Check the homologues and transform the one-to-one ones; for the many to one or vice-versa, we would have to deal with them with a specific rule;
• "Cross-align" the samples (Human to Mouse Genome, and vice-versa) and do two DEGS (for mouse genes & for human genes).

Since it is wildly unconventional, I am not sure at all about these options. Is there any pipeline and/or approach to this, reported, published,...? That would help me a lot.

Cheers

André