Welcome to Cedar-Sinai Medical Center Data Science Navigation team’s Galaxy documentation!

In this tutorial, the user will be guided through using a workflow in the Cedars-Sinai Galaxy instance. This workflow is for RNA-seq analysis, and covers Primary, Secondary and Tertiary analysis. In Galaxy, there are two workflows, “RNA-seq Primary analysis” which covers Primary and secondary analysis and “RNA-seq Tertiary analysis” which covers tertiary analysis. If you would like to access all tutorials developed for Galaxy workflows by the DSN team, it is accessible here.

Note

This project is under active development.

Contents

• RNA-seq introduction
• Quick-start
• Primary analysis
  • Using example data
  • Importing data
  • Quality check and read processing
  • Trimming raw reads
• Secondary Analysis
  • Alignment
  • Quantification of reads
  • Accessing results
• Tertiary Analysis
  • Importing data
    • Importing count data from Primary Analysis
    • Importing example data for running Tertiary Analysis
  • Analysis of differential gene expression
    • Identification of differentially expressed genes
    • DESeq2 output
    • Expression and annotation of differentially expressed genes
    • Visualization of the expression of differentially expressed genes
  • Functional enrichment analysis of DE genes
    • GO pathway analysis
    • goseq output
    • KEGG pathway analysis
  • Accessing results
• Supplementary section
  • Creating a data file
  • Obtaining files from Data Libraries
  • Files needed for RNA-seq workflows
• Conclusion