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Cell Ranger is a set of analysis pipelines that process Chromium single cell data to align reads, generate feature-barcode matrices and perform clustering and gene expression analysis  for 10X Genomics Chromium Technology[1].

Cell Ranger -

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ATAC in Partek Flow

The 'cellranger-atac count' pipeline from Cell Ranger v6ATAC v2.0.0[2] has been wrapped in Partek^® Flow^®  as Cell Ranger - Gene ExpressionATAC task. It does not comprehensively cover all of the options and analysis cases Cell Ranger can handle for now, but convertstakes FASTQ files from from 'cellranger-atac mkfastq' and performs ATAC analysis including reads filtering 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  identification of transposase cut sites, peak and cell calling, count matrix generation. Its outputs then becomes the starting point for downstream analysis for scRNAscATAC-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 -

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ATAC in Flow

To run the Cell Ranger - Gene ExpressionATAC task for scRNAscATAC-seq data in Flow, select Unaligned reads datanode, then select Cell Ranger - Gene ExpressionATAC in the 10x Genomics section (left panel, Figure 1). For Feature Barcode data, there will be two data nodes once the FASTQ files have been imported into Flow properly - mRNA and protein (right panel, Figure 1). Users should select mRNA datanode to trigger the Cell ranger - Gene Expression task. 

Once the Genomics production has been picked, users will be asked to create a Reference assembly if it is the first time to run the Cell Ranger - Gene Expression task (Figure 2). In Partek Flow, we will use Cell Ranger ARC 2.0.0 to create reference assembly for all 10x Genomics analysis pipelines. To create and use a reference assembly, Cell Ranger ARC requires a reference genome sequence (FASTA file) and gene annotations (GTF file), here is the details.

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