Single Cell Data Analysis

Output Description

In the following we describe the output files generated with our in-house pipeline scrnaseq2.

HTML report

  • Location: index.html
  • The HTML report contains various sections detailing the steps performed during the analysis of scRNA-Seq data. The various chapters included are:
    • Introduction: A brief introduction to the project, including the experimental design and research objective
    • Read data: The general staistics and metadata for the datasets
    • QC and filtering: The pre-filtering and post-filtering QC metrics and plots
    • Normalization: The normalization method and plots
    • Dimensionality reduction: The dimensionality reduction method and plots
    • Clustering and UMAP: The clustering and UMAP plots
    • Cluster QC: The cluster QC metrics and plots
    • Cluster Annotation: The cluster annotation and plots
    • Cluster Composition: The cluster composition and plots
    • Export data: The data export options

Results folders/files

  • Location: results/
  • cellxgene: Contains the cellxgene/cellxgene.h5ad for web-based exploration of single-cell data usingc CellxGene.
  • loupe (10x only): Contains the loupe/scrnaseq2.cloupe for interactive visualization and analysis using Loupe Browser
  • sc: Contains the Seurat object (with on disk directories): sc/sc.rds for further analysis in R using the Seurat package.
  • figures: Contains all the images generated as pdf and png files
  • metadata_qc.xlsx: Quality control metrics for each cell, such as number of genes detected, UMI counts, mitochondrial gene percentage, etc.
  • reduction_***_***.xlsx: Coordinates for each cell and the used reduction method
  • visualization_***_***.xlsx: Coordinates for each cell and the used visualization method
  • seurat_clusters.xlsx: Cluster assignments for each cell based on the Seurat clustering algorithm
  • markers.xlsx: Marker genes for each cluster, including statistics like p-values and fold changes
  • annotation_xxx.xlsx: Cell type annotations for each cell, if available

Module files

  • Location: modules/
  • The index.html consists of various modules/chapters. Each module/chapter has its own folder with results and figures.

Other files

  • All other files provide technical details and intermediate data required for reproducing the analysis and troubleshooting if needed.