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Identifying reads with matching UMIs and consolidating them into a single aligned read for use in quantification is handled by the Deduplicate UMIs task in Partek Flow. 

Default behavior

An important consideration when analyzing UMI data are the errors introduced into the UMIs themselves during PCR amplification of the original molecule. If these errors are not accounted for and each sequenced UMI is considered to be representative of the original UMI, the number of unique molecules can be significantly overestimated. To account for this, the Deduplicate UMIs task the Deduplicate UMIs task uses an implementation of the UMI-tools algorithm described in Smith et al. 2017.  

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Retain only one alignment per UMI

Deduplicate UMIs has UMIs has an alternative setting to more closely match methods used by CellRanger: Retain only one alignment per UMI. Selecting this option changes how the task functions and requires that you specify the genome assembly and gene/feature annotation.

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