Entering edit mode
11.3 years ago
kanwarjag
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1.2k
I have a RNA-seq data for viral genome and would like to see expression of UT vs treated samples. I was wondering which alignment should I be using regular Bowtie or BWA. I personally feel TopHat will not be good choice for Viral RNA-seq but not sure. Any suggestion please.
Thanks
Kanwar
Since viruses are small why not try all three methods and see what works best? I just used bowtie 2 for a dsDNA virus and it worked well.