How to add GFP sequence to mouse genome for mapping

[Kaizen]

Hi guys,
I was wandering what is the right way to add the sequence of GFP reporter to a mouse genom. Basically instead of "geneA" in the genome the modified mouse has "geneA-IRES-GFP".
I guess that adding just the sequence of GFP as an extra chromosome is not ideal, since a read that would map to both "geneA" and "IRES-GFP" would not be mapped by STAR.
Does anyone know what to do?
Thanks

[atpoint]

You could make an alternative genome by masking the exons of geneA in the fasta (so adding N instead of the actual sequence), and then add the transgene sequence as an extra chromosome.

[Kaizen]

but in that case, if you have a read mapping both to the transgene sequence and to the sequence upstream of downstream of it would lead to incorrect mapping and therefore will be lost, right?

[atpoint]

The read should be soft-clipped. Use BWA mem for alignment. Soft-clipping of reads is the basis of structural variant detection by many SV tools.