Metatranscriptomics Analysis of Microbial Communities

Welcome! This guide walks through end-to-end analysis of metatranscriptomic (mRNA) data from quality control to differential functional activity.

• 1. Overview
  • 1.1. Aim
  • 1.2. Inputs
  • 1.3. Outputs
  • 1.4. Pipeline Outline
• 2. Obtaining Data
  • 2.1. Public Repositories
  • 2.2. Example (SRA tools)
  • 2.3. Metadata
• 3. QC and Pre-processing
  • 3.1. Steps
  • 3.2. Example (fastp)
• 4. rRNA Depletion
  • 4.1. Tools
• 5. Mapping vs Assembly
  • 5.1. Mapping-first
  • 5.2. Assembly-first
• 6. Functional Profiling
  • 6.1. Goal
  • 6.2. Tools
  • 6.3. Normalization
  • 6.4. Outputs
• 7. Taxonomic Profiling (Optional)
  • 7.1. Goal
  • 7.2. Approaches
  • 7.3. Result
• 8. Differential Analysis
  • 8.1. Input
  • 8.2. Model
  • 8.3. Tools
  • 8.4. Visualizations
• 9. References and Further Reading