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What is Cell Ranger?

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 - ATAC in Partek Flow

The 'cellranger-atac count' pipeline from Cell Ranger ATAC v2.0[2] has been wrapped in Partek^® Flow^®  as Cell Ranger - ATAC task. It takes FASTQ files from 'cellranger-atac mkfastq' and performs ATAC analysis including reads filtering and alignment, barcode counting, identification of transposase cut sites, peak and cell calling, count matrix generation. Its outputs then becomes the starting point for downstream analysis for scATAC-seq data in Flow. 

Running Cell Ranger - ATAC in Flow

To run the Cell Ranger - ATAC task for scATAC-seq data in Flow, select Unaligned reads datanode, then select Cell Ranger - ATAC in the 10x Genomics section (Figure 1). 

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Cell Ranger - Gene Expression task report in Flow

Task report is sample based. Users can use the dropdown list on the top left to switch samples.  Under the sample name, there are two tabs on each report - Summary report and Analysis report (Figure 7).  Important information on Estimated Number of Cells, Mean Reads per Cell, Median Genes per Cell, as well as information on Sequencing, Mapping, and Sample are summarized in different panels. The Barcode Rank Plot has also been included as an important piece in the Cells panel in the Summary report (Figure 7). 

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Memory limit (GB): Restricts Cell Ranger - Gene Expression to use specified amount of memory (in GB) to execute pipeline stages. 

References

1. https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome

2. https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/6.0/release-notes

3. https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/4.0/release-notes
4. https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis#feature-ref

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