ReDeeM: single-cell Regulatory multi-omics with Deep Mitochondrial mutation profiling. ReDeeM is a single-cell multiomics platform featuring ultra-sensitive mitochondrial DNA (mtDNA) variant calling and joint RNA+ATAC profiling. ReDeeM enables fine-scale lineage tracing at single cell level, allowing for subclonal and phylogenetic analyses, with simultaneous integrative analyses of cell-state and gene regulatory circuits.

The analytical pipelines for ReDeeM analysis includes two parts:

• redeemV is set of in-house Bash pipeline and python scripts for mapping and deep mitochondrial mutation calling. (This page, Input from rawdata)
• redeemR is an in-house R package for downstream lineage tracing and single cell integrative analysis. (Input from redeemV)

redeemV is a streamlined pipeline taking advantage of endogenous unique molecular identifier (eUMI) for consensus-based error correction in single-cell mitochondrial DNA mutation detection.

redeemV includes a set of ready-to-use Bash pipeline and Python scripts

git clone https://github.com/chenweng1991/redeemV.git

Please check the tutorial (A small set of example fastq files are included)

• ReDeeM data structure
• Run Cellranger-arc
• Cell hashing processing

Please check out our study of human hematopoiesis using ReDeeM Deciphering cell states and genealogies of human hematopoiesis

If you have any questions or suggestions, please feel free to contact us. Feedbacks are very welcome! (Chen Weng, [email protected])