Are the HAP1 cell lines complete knockouts?
The clonal cell line you obtain bears a frameshift mutation in your gene of interest. For this reason, we do not expect any residual gene expression of the wild-type allele. However, there are two rare scenarios in which such expression of the wild-type allele may still be detectable: There is an alternative start codon downstream of the actual ATG. There is an alternatively spliced transcript that does not include the edited exon.