In the methods of this paper, the authors say:
Reads were then filtered based on quality score in the UMI region. Any read with >1 low-quality base (phred <=10) were discarded. Reads with more than one mismatch in any of the three 8 nt cell barcodes were also discarded. The cDNA reads (Read 1) were then mapped to either a combined mm10- hg19 genome or the mm10 genome using STAR (44).
I understand how to filter based on mismatch after mapping but in this case it is done before mapping. Has this to be interpreted as "Reads with low quality in more than one base in any of the three 8 nt cell barcodes were also discarded"?