ScSmOP Supported Technology - ZhengmzLab/ScSmOP GitHub Wiki
ScSmOP support following types of data
| Omics | Technology | Barcode(s) length | UMI length | Read structure | Method ID (-t) | Source Barcode |
|---|---|---|---|---|---|---|
| scRNA-seq | 10× Genomics (v2) Single Cell Gene Expression | 16 | 10 | R1: Barcode-UMI; R2: Transcript | scrna_10x_v2 | https://github.com/10XGenomics/cellranger/raw/master/lib/python/cellranger/barcodes/737K-august-2016.txt |
| scRNA-seq | 10× Genomics (v3) Single Cell Gene Expression | 16 | 12 | R1: Barcode-UMI; R2: Transcript | scrna_10x_v3 | https://github.com/10XGenomics/cellranger/raw/master/lib/python/cellranger/barcodes/3M-february-2018.txt.gz |
| scRNA-seq | Drop-seq | 12 | 8 | R1: Barcode-UMI; R2: Transcript | dropseq | https://github.com/minoda-lab/universc/tree/master/test/shared/dropseq-test |
| ChIA-Drop | ChIA-Drop | 16 | N/A | R1: Barcode-DNA; R2: DNA | chiadrop | longranger-2.2.2/longranger-cs/2.2.2/tenkit/lib/python/tenkit/barcodes/4M-with-alts-february-2016.txt |
| scATAC-seq | 10× Genomics (v2) Single Cell ATAC | 16 | N/A | R1: DNA; R2: Barcode; R3: DNA | scatac_10x_v1 | cellranger-atac-2.1.0/lib/python/atac/barcodes/737K-cratac-v1.txt.gz |
| SPRITE and derivates | SPRITE | 4 kinds with 5 rounds | N/A | R1: DPM-DNA; R2: Y-ODD-EVEN-ODD | sprite | GSE114242: GSE114242_human_config.txt.gz |
| SPRITE and derivates | RD-SPRITE | 5 kinds with 5 rounds (label DNA with DPM, label RNA with RPM) | N/A | R1: DNA/RNA; R2: Y-ODD-EVEN-ODD-DPM/RPM (DPM: DNA, RPM: RNA) | rdsprite | https://github.com/GuttmanLab/sprite2.0-pipeline/blob/master/config.txt |
| SPRITE and derivates | Single-cell SPRITE | 4 kinds with 6 rounds (label cells with first last 3 barcodes in Read 2, label complex with all six barcodes) | N/A | R1: DNA; R2: Y-EVEN-ODD-EVEN-ODD-DPM | scsprite | https://github.com/caltech-bioinformatics-resource-center/Guttman_Ismagilov_Labs/blob/master/scSPRITE/misc/config_dpm6_y-stag_scSPRITE.txt |
| scARC-seq | 10× Genomics Single Cell Multiome ATAC + Gene Expression | Gene Expression library: 16, ATAC library: 16 | Gene Expression library: 12; ATAC library: N/A | R1: DNA (R1 in ATAC); R2: Barcode (R2 in ATAC); R3: DNA (R3 in ATAC); R4: Barcode-UMI (R1 in GEX); R5: Transcript (R2 in GEX) | scarc_10x_v1 | 737K-arc-v1-scrna.txt:cellranger-arc-2.0.2/lib/python/cellranger/barcodes/737K-arc-v1.txt.gz; 737K-arc-v1-scatac.txt:cellranger-arc-2.0.2/lib/python/atac/barcodes/737K-arc-v1.txt.gz |