Xavier Lab Documentation

• Introduction
• Setup
  • Google Cloud Setup
    • General Information
    • Web Access
    • Command Line Access
    • Authentication
    • Recommended Usages
    • Q&A
    • Further Reading
    • Notes
  • FireCloud Setup
    • What is FireCloud?
      • Workspaces
      • Methods
      • Groups
    • When/why to use FireCloud
    • Setting Up Billing
    • Creating and Adding to Groups
    • Accessing Google Cloud Buckets
• Pipelines
  • Pipeline Usage Information
    • Firecloud GUI
      • Job Submission
    • Command Line
    • Building/Editing a Pipeline
      • Editing a WDL
      • Editing a Docker container
  • bcl2fastq Pipeline
    • Overview
    • Setup
      • Configuration
        • experiment_name
        • experiment_type
  • Bulk RNA-Seq Pipeline
    • Overview
    • Setup
      • Preprocessing
      • Configuration
        • experiment_name
        • experiment_type
        • input_data_type
        • organism
        • reference_transcriptome
        • read_pairs_file
        • samples_described_file
        • samples_compared_file
      • SampleSheet.csv
    • Output
      • kallisto_output
      • edgeR_output
      • multiqc_report.html
    • Troubleshooting
  • STARS CRISPR Screen Pipeline
    • Overview
    • Setup
      • Preprocessing
      • Configuration
        • experiment_name
        • library_name
        • runs
        • condition_file
        • samples_described_file
        • samples_compared_file
    • Output
      • analysis
      • stars_output
    • Troubleshooting
• Utilities
• Broad Server
  • General Tips
    • Using the Broad Server
    • Broad IT Support
  • Available Nodes
    • Login Nodes
    • Lab-Owned Nodes
  • Software
    • Dotkits
    • Shell Configuration
  • Data
    • Host
    • Microbiome
• Miscellaneous
  • Contributing
    • Adding or editing a pipeline
    • Adding utilities
    • Contributing to documentation
      • General Structure
      • Tips
    • Comments/Concerns
  • Acknowledgements and Getting Help