Can I Use Tophat To Align Exome Seq

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?

exome seq

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written 14.0 years ago by camelbbs

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

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written 14.0 years ago by Sean Davis

3 answers

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

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written 14.0 years ago by Zev.Kronenberg

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

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written 14.0 years ago by JC

thanks guys! ..

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written 14.0 years ago by camelbbs

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