Meaning of UMI_cor = 2 in sc_gene_counting()

[PeteHaitch]

I'm having a hard time understanding the documentation of UMI_cor = 2 in sc_gene_counting()

correct UMI sequencing error: 0 means no correction, 1 means simple correction and merge UMI with distance 1. 2 means merge on both UMI alignment position match.

Could you please clarify?

[LuyiTian]

for UMI_cor = 1, all UMIs that mapped to the same genes are grouped together and duplicated UMIs are removed.

for UMI_cor = 2, all UMIs that mapped to the same genes and in the same positions are grouped together and duplicated UMIs are removed. so UMI_cor assume that one molecule, after amplification, would only generate the same fragment.
Later on, I realized it is rarely the case and most protocols, including 10X and CEL-seq2, involves pre-amplification before the full-length cDNAs are cut down to fragments. So there could be more than one fragment for the one mRNA molecule. I did'not delete it in case it is useful in some special situation. But for the most time, it should not be used.

[PeteHaitch]

Thanks, Luyi. So UMI_cor = 1 is the recommended value?
I think it would be useful to update the documentation with those extra details and ensure the default value matches the most common protocol(s).
Aside: a description of UMI_cor = 2 is missing from create_report():

scPipe/R/sc_workflow.R

Lines 203 to 211 in 02e9784

	if (UMI_cor == 1) {
	tx = gsub(pattern = "UMI_COR__", replacement = "simple correction and merge UMI with distance 1", x = tx)
	}
	else if (UMI_cor == 0) {
	tx = gsub(pattern = "UMI_COR__", replacement = "no correction", x = tx)
	}
	else {
	tx = gsub(pattern = "UMI_COR__", replacement = "unknown", x = tx)
	}