Data Preprocessing Requirements

Count Matrix Generation

Before using the Nygen, your sequencing data must be processed into count matrices. This preprocessing step typically involves:

1. Converting raw sequencing data (FASTQ files) into gene expression matrices
2. Processing through standard bioinformatics pipelines such as:
   • Cell Ranger (for 10x Genomics data)
   • alevin/alevin-fry
   • kallisto|bustools
   • STARsolo
   • zUMIs

The platform accepts count matrices from any single-cell technology, provided they are properly formatted.

‍

Technical Requirements

Browser Requirements

• Recommended Browsers:
  • Google Chrome (latest version)
  • Microsoft Edge (latest version)
• No specific plugins or extensions required
• Default browser settings are sufficient
• Active internet connection required

Account Setup

• Use your institutional email address to signup and get a generous freemium
• No credit card required for account creation
• Choose your default server location during initial setup
• Default server location can be changed later if needed

‍