The Deduplicate UMIs task identifies and removes reads with duplicate unique molecular identifiers (UMIs). The methods available for UMI deduplication are outlined in our UMI Deduplication in Partek Flow white paper. 

To invoke Deduplicate UMIs:

• Click an Aligned reads data node
• Click Post-alignment tools in the toolbox
• Click Deduplicate UMIs

The task configuration dialog content depends on whether you imported FASTQ files or BAM files into Partek Flow.

Imported FASTQ

UMIs and barcodes are detected and recorded by the Trim tags task in Partek Flow. You can choose whether to retain only one alignment per UMI or not. The default will depend on which prep kit was used in the Trim tags task. 

If you select Retain only one alignment per UMI, you will be asked to choose an assembly and gene/feature annotation file. The annotation file is used to check whether a read overlaps an exonic region. 

Imported BAM

UMIs and barcodes are stored in the BAM header. Additional options are available in the task configuration dialog to allow you to specify the location of the UMI and barcode information in the BAM header. 

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