Question

Can I Use Tophat To Align Exome Seq

0

Entering edit mode

11.8 years ago

camelbbs ▴ 710

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 • 2.7k views

ADD COMMENT • link 11.8 years ago by camelbbs ▴ 710

1

Entering edit mode

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

ADD REPLY • link 11.8 years ago by Sean Davis 26k

score 2 · Answer 1 · 2012-08-02

2

Entering edit mode

11.8 years ago

Zev.Kronenberg 12k

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

ADD COMMENT • link 11.8 years ago by Zev.Kronenberg 12k

score 1 · Answer 2 · 2012-08-02

1

Entering edit mode

11.8 years ago

JC 13k

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

ADD COMMENT • link 11.8 years ago by JC 13k

score 0 · Answer 3 · 2012-08-02

0

Entering edit mode

11.8 years ago

camelbbs ▴ 710

thanks guys! ..

ADD COMMENT • link 11.8 years ago by camelbbs ▴ 710