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

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

rna-seq
• 4,729 views • link
updated by David Langenberger David Langenberger • written by kanwarjag kanwarjag

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.

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written by Zev.Kronenberg Zev.Kronenberg

3 answers

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

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written by swbarnes2 swbarnes2

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

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written by David Langenberger David Langenberger

Bowtie 2 worked great

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written by kanwarjag kanwarjag

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