6.3 years ago by
I have a different answer than JC, although I actually agree with him. If you look at the tophat paper (Trapnell, Pachter & Salzberg, 2009), you'll see that tophat is a gapped read aligner that first uses bowtie to map reads to the genome, and then it uses the resulting read pile ups to build a potential splice database, and then it takes all the reads that did not align the first time, and sees if any of them can align if they are split between read piles. Thus, in general, if you simply want to map DNA-Seq reads for whole genome mapping, as JC points out tophat would be pointless. However, if you had reason to believe that your reference genome contains lots of gaps, then it seems tophat could be used to potentially detect gap differences between your sequenced genome, and your reference genome. There is some evidence that some genomes (i.e. flatworm) may contain many locations with small gaps, and these gaps are highly heterologous between individuals.