tophat2 RNAseq mapping to haplogenomes
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
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