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Cell Ranger v6.0.0[2] has been wrapped in Partek^® Flow^®  as Cell ranger 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. 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.

Note: when use Cellranger Cell ranger task in Partek Flow, there is more restrictions on sampe name-- sample name can only contains contain letters, digits, underscores and dashes. Please Edit the sample name names on Data tab in Partek Flow to remove any other characters ,e.g. space etc.

Running Cell ranger in Flow

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