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Cell Ranger - Gene Expression in Partek Flow

The 'cellranger count' pipeline from Cell Ranger v6.0.0[2] has been wrapped in Partek^® Flow^®  as Cell Ranger - Gene Expression task. It does not comprehensively cover all of the options and analysis cases Cell Ranger can handle for now, but converts FASTQ files from cellranger mkfastq and performs alignment, filtering, barcode counting, UMI counting for single cell gene expression and Feature Barcode data. The output gene expression count matrix in .h5 format (both raw and filtered available for users to download in the output page of task details) then becomes the starting point for downstream analysis for scRNA-seq in Flow. For Feature Barcode data, Flow outputs a unified feature-barcode matrix that contains gene expression counts alongside Feature Barcode counts for each cell barcode.

Note: When use Cell Ranger - Gene Expression task in Partek Flow, there are more restrictions on sample name -- sample name can only contain letters, digits, underscores and dashes. Please edit the sample names on Data tab in Partek Flow to remove any other characters ,e.g. space etc.

Running Cell Ranger - Gene Expression in Flow

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Users will be asked to create a Cell Ranger 6.0.0 reference genome if it is the first time to run the Cell rangerRanger - Gene Expression task in Flow (Figure 2). 

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