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Old 12-03-2012, 09:33 AM   #9
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Originally Posted by mathew View Post
Thanks swbarnes2,

I agree, so what I have done is I have aligned with just viral genome that is not very good (around 0.3% aligned reads). Then when I aligned to a combined human and viral genome it gives me around 70% aligned reads. However I am not sure how I can separate out the reads aligned to viral genome only.
Samtools view is how you do that.
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