Aligning RNA-seq reads to the personal genomes instead of the Reference Genome

[var]

I wish to align RNA-seq reads to the corresponding genomes instead of the reference genomes to see the difference between the two approaches. I am planning to use Bowtie Build for generating the index files and then using Tophat to align the reads. I haven't come across any such thread and would really appreciate inputs from people who've had experience with a similar approach.

Thanks!

[westerman]

Certainly it is easy to use different genomes with Tophat. But I do not see what using 'personal genomes' versus the reference genome will get you since the reference genome is undoubtedly more complete and better annotated than any non-reference genome.

Perhaps if you explain your reasoning a bit more then the rest of us could give more input.