I would like to add a human gene sequence to a mouse reference genome

Question

[Apprentice]

A human gene X was introduced into a mouse by transfection.

I extracted mRNAs from the organs of this mouse and would like to measure the expression level of human gene X by RNA-seq. To do the analysis of the RNA-seq data , I need to add the mouse genome sequence with the human gene X sequence added to it as a reference genome.After that, I need to perform mapping using the new reference genome. Thus, is it possible to create a new reference genome in which a specific sequence of human (from GRCh38) is added to the conventional reference genome of mouse (GRCm38)?

Answer 1

[d-cameron]

Thus, is it possible to create a new reference genome in which a specific sequence of human is added to the conventional reference genome of mouse?

It is indeed entirely possible but you need to be wary of the mouse homolog of the transgene. Make sure any RNA quantification you do correctly differentiates human reads, mouse reads, and ambiguous reads that could have come from the human or mouse homolog because that particular region of the gene is highly similar/identical.

[Apprentice]

Thank you for your prompt feedback. What would be the best way to realize what you advise? Are there any tools or commands that would facilitate the realization? I would appreciate it if you could enlighten me.