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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) then becomes the starting point for downstream analysis for scRNA-seq in Flow.

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Clicking the big grey button of Create Cell Ranger 6.0.0 reference would pop up a new window where lists the three pre-built reference genomes for human(hg38), mouse(mm10) and the both mixed genome mix of two(hg38-mm10), respectively (Figure 3). They are exactly the same reference genomes (2020-A) that are provided in Cell Ranger by default. In details, the transcriptome annotations are respectively GENCODE v32  for human and vM23 for mouse, which are equivalent to Ensembl 98[3]. References for other organisms currently are not available in Flow Cell ranger, and will be coming in the next version.

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