DRAGEN Single-Cell RNA Pipeline

The DRAGEN Single-Cell RNA (scRNA) Pipeline can process multiplexed single-cell RNA-Seq data sets from reads to a cell-by-gene UMI count gene expression matrix. The pipeline is compatible with library designs that have one read in a fragment match to a transcript and the other containing a cell-barcode and UMI. The pipeline includes the following functions:

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RNA-Seq (splice-aware) alignment and matching to annotated genes for the transcript reads.

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Cell-barcode and UMI error correction for the barcode read.

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UMI counting per cell and gene to measure gene expression.

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Sparse matrix output and QC metrics.

The functionality and options related to alignment and gene annotation are identical to the RNA-Seq pipeline. For information, see DRAGEN RNA Pipeline. Other RNA-Seq modules, such as gene fusion calling or transcript-level gene expression quantification are not supported for Single-Cell RNA.