Overview

1. Overview#

1.1. Aim#

Measure actively transcribed functions in microbial communities and link expression to taxa and pathways.

1.2. Inputs#

  • Raw paired-end RNA-seq FASTQ files (rRNA-depleted)

  • Metadata (samples, treatments)

  • Optional reference genomes or gene catalogs

1.3. Outputs#

  • QC metrics

  • rRNA removal stats

  • Counts mapped to genes/pathways

  • Differential activity results

  • Visualizations

1.4. Pipeline Outline#

  1. Data access (SRA/ENA) & metadata

  2. QC & pre-processing (quality trimming, adapters)

  3. rRNA depletion in silico (if needed)

  4. Read mapping vs. assembly strategy

  5. Functional profiling (gene/pathway quantification)

  6. Taxonomic profiling (optional, expression-weighted)

  7. Differential analysis & visualization

Contents