Can I Use Tophat To Align Exome Seq

Question

[camelbbs]

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?

[Sean Davis]

TopHat uses bowtie (or bowtie2) as the underlying alignment engine. Bowtie2 would be appropriate, but not TopHat.

Answer 1

[Zev.Kronenberg]

Nope, you do not want to use tophat to align exome data as it is captured DNA, and not RNAseq.

Answer 2

[JC]

No, please first try to understand what are you trying to analyze: http://en.wikipedia.org/wiki/Exome_sequencing

Answer 3

[camelbbs]

thanks guys! ..