Discrepancies in results using scaffolded assemblies
Hi,
I have an assembly made with ONT data, and then I used Hi-C to scaffold the assembly. I run BUSCO v5 on both assemblies. According to the results, there were 11 genes that were present in the ONT but not in the Hi-C assembly, and 8 genes that were fragmented in the Hi-C but complete in the ONT assembly.
All the regions from which these genes were annotated are present in both assemblies at 100% coverage and 100% identity. Is there a reason why these genes show different status even though the regions are present in both?
Cheers, Georgios