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Old 12-03-2012, 07:31 AM   #7
mathew
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Location: australia

Join Date: Jan 2011
Posts: 81
Default Viral genome

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. It may be that most of reads are mapped to human. As far as no of viral particles in that library are concerned the experiment has worked and mostly the induction is by viral infection which has translated well into human genome analysis. Any thought on how we can I get viral genome reads only? I have read papers which state that they just aligned to viral genome and then called peaks but it is not working in my case unless I am missing something.

Thanks
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