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Most single cell RNA-seq library prep kits compensate for the small quantity of starting material by PCR amplifying the reverse transcribed cDNA. Because some sequences will amplify preferentially, the final 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 nucleotide sequences, termed unique molecular identifiers (UMIs), prior to amplification. 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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