Hello everyone,
I have more of a general pre-processing question. We are doing some small viral genome sequencing. The virus is ssRNA (coronaviridae) and we have been using the RNAseq method on the PGM and I was just wondering if I'm doing the pre-processing correctly.
I have been treating the reads like genomic DNA for the processing, which is just mapping to the reference and marking duplicates. Is this correct? Should I be looking for splits? I know that viruses have different splices to make early and late proteins, but not really these two genes make one protein splices.
The more I thought about it the more unsure I became, does anyone have an opinion?
I have more of a general pre-processing question. We are doing some small viral genome sequencing. The virus is ssRNA (coronaviridae) and we have been using the RNAseq method on the PGM and I was just wondering if I'm doing the pre-processing correctly.
I have been treating the reads like genomic DNA for the processing, which is just mapping to the reference and marking duplicates. Is this correct? Should I be looking for splits? I know that viruses have different splices to make early and late proteins, but not really these two genes make one protein splices.
The more I thought about it the more unsure I became, does anyone have an opinion?
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