Dear seqanswers community,
I am currently planning a project on DNA sequencing of virus (probably using Illumina) and have a technical issue I would like to share with you.
I am aiming at comparing the diversity of a honey bee RNA virus (Deformed Wing Virus, or DWV) in several population of bees. Genomes of viral strains and recombinants are currently available (~10kb).
To do so, we (me and colleagues) are thinking of generating and sequencing cDNA. However, we want to get rid of as much honeybee DNA as possible in the final sequences. So, we are considering two options:
_ Multiple PCRs covering the whole virus genome to increase its proportion in the final yield
_ A few PCRs of the regions (~800-1000bp) where recombination is occuring (based on previous work) to focus on those interesting areas
It seems like the best way to have as much DWV sequences at the end. However, we are fairly new to the field. Is there anything we are missing here, or a better way to conduct our project?
Thanks a lot,
Alex
I am currently planning a project on DNA sequencing of virus (probably using Illumina) and have a technical issue I would like to share with you.
I am aiming at comparing the diversity of a honey bee RNA virus (Deformed Wing Virus, or DWV) in several population of bees. Genomes of viral strains and recombinants are currently available (~10kb).
To do so, we (me and colleagues) are thinking of generating and sequencing cDNA. However, we want to get rid of as much honeybee DNA as possible in the final sequences. So, we are considering two options:
_ Multiple PCRs covering the whole virus genome to increase its proportion in the final yield
_ A few PCRs of the regions (~800-1000bp) where recombination is occuring (based on previous work) to focus on those interesting areas
It seems like the best way to have as much DWV sequences at the end. However, we are fairly new to the field. Is there anything we are missing here, or a better way to conduct our project?
Thanks a lot,
Alex
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