Alexandria: Single-Cell Data Portal

Introduction

• The Alexandria Project
  • Background
  • Why use Alexandria?
  • Data upload
    • Types of studies:
    • Upload from Single Cell Portal file formats
• The Alexandria Metadata Convention
  • Metadata categories
    • Ontology-valued metadata
    • Numeric-valued metadata
    • Boolean-valued metadata
    • Controlled-list metadata
    • Free text-valued metadata
  • Metadata with complex dependencies
    • Dependent metadata
    • Array valued metadata

Workflows

• Running on Alexandria
  • Known Bugs
  • 1. Sign in
  • 2. Create a new study
  • 3. Uploading sequence data files
  • 4. Creating and uploading your Alexandria Sheet
  • 5. Configure and launch dropseq_cumulus workflow
  • 6. Advice for troubleshooting
  • 7. Synchronizing and exploring visualization options
• Running on Terra
  • Known Bugs
  • 1. Sign in
  • 2. Create a new workspace.
  • 3. Add your sequence data
  • 4. Creating and uploading your Alexandria Sheet
  • 5. Import the dropseq_cumulus workflow
  • 6. Configure and launch dropseq_cumulus workflow
  • 7. Advice for troubleshooting
  • 8. Uploading Cumulus output files to Alexandria for visualization
• Inputs/Outputs
  • The Alexandria Sheet
    • Formatting your Alexandria Sheet for FASTQ files
    • Formatting your Alexandria Sheet for bcl2fastq
    • Understanding the fastq_directory parameter
  • Inputs of the dropseq_cumulus workflow
    • Basic usage
    • Advanced usage
    • Optional inputs exposed on Terra
  • Outputs of the dropseq_cumulus workflow
• Drop-Seq Custom Genome

Notebooks

• Terra Notebooks
  • Background
  • Visting your Terra workspace from your Alexandria study
  • Uploading an Alexandria notebook and customizing your notebook runtime

Appendix

• Bcl2Fastq Docker Image
  • What is Docker?
  • Instructions
• Alternatives for uploading data
  • Terra
    • Google Bucket interface
    • Terra Data tab
  • Alexandria
    • Google Bucket interface
    • Upload & Save File button