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In droplet-based single cell isolation and library prep methods, each droplet is labeled by a unique nucleotide barcode. Because not all droplets will contain cells, it is important to filter out nucleotide barcodes that correspond to empty droplets prior to downstream analysis.

In Partek Flow, cell barcode you can filter barcodes interactively using a knee plot after UMI deduplication in the UMI deduplication task report or after quantification in the Cell barcode QA/QC task report. Alternatively, you can filter with using preset options using in the Filter barcodes task.

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The automatic filter threshold is set for each sample individually. It picks the cutoff between cells and empty droplets by identifying where the UMI content per barcode drops precipitously when moving in descending order from the barcode with the highest number of UMIs. 

Number of cells

Set the number of cells per sample to include. This is set for all samples; if set to 100, the top 100 barcodes by total UMI count for each sample will be retained. 

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