RNA-Seq mapping to a genome vs transcriptome?

[bob-loblaw]

Hi All,


I'm currently looking at putting together a reference database for mapping my RNA-Seq reads and I was wondering what people think is the best way to go. I was thinking about mapping directly to the genomes, from what I've heard this is much simpler. But that database would be a lot bigger, and hence take a lot longer for mapping. Mapping to the transcriptome does seem a bit more complicated, but it is doable. I was just wondering if anyone could offer some advice on if one has advantages over the other?

Thanks

EDIT: Just saw this is a duplicate, I requested it be deleted, sorry, my bad.