i see exome seq are most aligned by bwa, but can i use tophat to align it. tophat is designed to rnaseq, but exome seq is also from the exon region, right?
TopHat uses bowtie (or bowtie2) as the underlying alignment engine. Bowtie2 would be appropriate, but not TopHat.
Nope, you do not want to use tophat to align exome data as it is captured DNA, and not RNAseq.
No, please first try to understand what are you trying to analyze: http://en.wikipedia.org/wiki/Exome_sequencing
thanks guys! ..