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Old 12-02-2012, 12:55 PM   #6
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Ideally, if you know your samples has both human and viral sequence in it, you should be aligning to a reference that has both. That will give you the most accurate alignment.

Would you expect the antibody to be binding to viral sequence?

If you are getting very few reads aligning to virus, the simplest explanation is that you have very little virus in your library. Why have you dismissed that possibility?
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