Cellranger count performs some basic quality filtering and error correction for UMI sequencing errors.

 

The following criteria are used for UMI filtering:
 
– Must not be a homopolymer, e.g. AAAAAAAAAA
– Must not contain N
– Must not contain bases with base quality < 10
 
UMIs that are 1 Hamming distance (substitution) away from a higher-count UMI are corrected to the higher count UMI if they share a cell barcode.