Question: Can I Use Tophat To Align Exome Seq
0
gravatar for camelbbs
6.7 years ago by
camelbbs650
China
camelbbs650 wrote:

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 • 1.8k views
ADD COMMENTlink written 6.7 years ago by camelbbs650
1

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

ADD REPLYlink written 6.7 years ago by Sean Davis25k
2
gravatar for Zev.Kronenberg
6.7 years ago by
United States
Zev.Kronenberg11k wrote:

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

ADD COMMENTlink modified 6.7 years ago • written 6.7 years ago by Zev.Kronenberg11k
1
gravatar for JC
6.7 years ago by
JC7.7k
Mexico
JC7.7k wrote:

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

ADD COMMENTlink written 6.7 years ago by JC7.7k
0
gravatar for camelbbs
6.7 years ago by
camelbbs650
China
camelbbs650 wrote:

thanks guys! ..

ADD COMMENTlink written 6.7 years ago by camelbbs650
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