I noticed that in the nimble output, there are rows with either empty feature names, or what seems like an empty value concatenated with others (i.e. trailing comma: "NKG2A,NKG2D,"). This shouldnt happen. my best guess is that perhaps this is due to collapsing by lineage? Perhaps some references lack a value for lineage? In this situation, we should coalesce from the lineage field back to the original name. I dont know if this is actually the cause, and I guess it's possible that instead some reads had zero alignments, and it's treating no alignments like empty string?
Anyway, see this example, which used the NCR library, coalescing on lineage:
I noticed that in the nimble output, there are rows with either empty feature names, or what seems like an empty value concatenated with others (i.e. trailing comma: "NKG2A,NKG2D,"). This shouldnt happen. my best guess is that perhaps this is due to collapsing by lineage? Perhaps some references lack a value for lineage? In this situation, we should coalesce from the lineage field back to the original name. I dont know if this is actually the cause, and I guess it's possible that instead some reads had zero alignments, and it's treating no alignments like empty string?
Anyway, see this example, which used the NCR library, coalescing on lineage:
https://prime-seq.ohsu.edu/experiment/Labs/Bimber/653/showFile.view?rowId=6903002&inline=true