I have a Gene mapping of a virus segment mapping to the reference gene. I mapped the gene segment to the reference gene using the Map to reference tool in CLC workbench. I see that this a possibility of two alleles mapping to the same reference gene mostly due to the possibility that both the gene segments are very similar to each other with some SNP changes between the segments. My problem is, how do I separate the 2 alleles into their own gene segment.
I thought doing a denovo assembly of the reads shall help me to separate the 2 segments, however I have been unable to separate them through this route. I have tried the assembler in CLC, Geneious and SPAdes for the denovo assembly.
Kindly help.
Please let me know if I need to provide additional information and I am more than happy to do so.
