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:

RNA-Seq (splice-aware) alignment and matching to annotated genes for the transcript reads.
Cell-barcode and UMI error correction for the barcode read.
UMI counting per cell and gene to measure gene expression.
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.