Most single cell RNA-seq library prep kits compensate for the small quantity of starting material by PCR amplifying the reverse transcribed cDNA. Because sequences will amplify with varying avidity, the proportions of PCR amplified molecules will diverge from the original number of molecules. To correct for these PCR artifacts, reverse transcribed molecules are tagged with unique molecular identifiers (UMIs). These UMIs are retained through PCR amplification, allowing PCR products that were amplified from the same original molecule to be identified. Counting UMIs for each gene instead of reads allows the original number of molecules corresponding to each gene to be more faithfully represented.

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