Single Cell Long Read Transcriptome

Wf-single-cell

• Data QC
• Identify the cell barcode and UMI sequences present in Nanopore sequencing reads
• Summary metrics (read quality, number of cells, genes and transcripts identified within each sample, median genes per cell, and sequence saturation)
• UMAP projections

Cell Ranger

• Demultiplex BCL files from a sequencer into FASTQs
• Summary metrics (sequencing quality, number of cells detected, the mean reads per cell, and the median genes detected per cell et al.)
• Alignment of reads to genome
• Gene expression quantification
• Clustering analysis
• Differentially expression analysis between clusters
• Visualization

• Data QC
• Mapping and Quantification
• Dimensionality reduction, clustering, and differential analysis
• Base on gene
  Base on transcripts
• GO/KEGG/Reactome Enrichment Analysis
• Alternative Splicing

• Demultiplex BCL files from a sequencer into FASTQs
• Alignment, UMI counting, Metrics summary
• Identification of highly variable gene (HVGs)
• Cell Subpopulation Identification
  Principal component analysis (PCA)
  Identify clusters of cells
  Dimensionality reduction and Visualization
• Marker gene detection (Differentially expression analysis between clusters)
• GO/KEGG/Reactome Enrichment
  Functional Annotation of Transcription Factor
  Protein-Protein Interaction Network Analysis