Which Aligner Is Most Suited For Viral Rna-Seq Data?

Question

[kanwarjag]

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

[Zev.Kronenberg]

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.

Answer 1

[swbarnes2]

The differences between the two aligners will be tiny, so just use the one you are most familiar with.

Answer 2

[David Langenberger]

I would recommend segemehl, since it can map split-reads. This way you can find circularized RNAs, which is very interesting, especially in viruses.

Answer 3

[kanwarjag]

Bowtie 2 worked great