tophat2 RNAseq mapping to haplogenomes

Question

[m.eitel]

Hello

I am wondering how to use tophat2 to map RNAseq data to the haplogenomes of my sequenced species? That is which options do I need to set to allow mapping of the RNA reads to both (almost identical) copies of the genome so that I end up with transcripts (after stringtie) on both haplocontigs instead of just one?

Thanks Michael