Metatranscriptomics & Active Community Inference — Hands-on

Learn how to move from DNA based community snapshots to RNA level views of microbial activity. This module covers metatranscriptomic study design, RNA handling, rRNA and host depletion, mapping strategies, expression quantification, and active community inference, with practical workflows that integrate with metagenomic and functional profiling modules.

Metatranscriptomics & Active Community Inference

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Session Index

Session 1 — Metatranscriptomics Design & RNA Handling Session 2 — Preprocessing, rRNA/Host Depletion & Mapping Session 3 — Expression Quantification & Active Community Inference Session 4 — Mini Capstone: Activity Profiles & Interpretation

Session 1

Fee: Rs 8800

Metatranscriptomics Design & RNA Handling

When and why to use metatranscriptomics

activity vs potential linking DNA and RNA signals clinical, environmental and AMR use cases

Study design and sampling for RNA integrity

stabilization reagents and cold chain time sensitive sampling paired DNA and RNA collections

RNA extraction, DNase and library strategy overview

microbial RNA extraction challenges DNase treatment rationale rRNA depletion vs mRNA enrichment concepts

Session 2

Fee: Rs 11800

Preprocessing, rRNA/Host Depletion & Mapping

QC and trimming for metatranscriptomic reads

FastQC / MultiQC review adapter and quality trimming length and complexity checks

In silico rRNA and host read depletion

mapping to rRNA databases sortmerna / bbsplit style tools human and host genome filters

Mapping strategies for metatranscriptomes

mapping to reference genomes and gene catalogs alignment vs pseudoalignment (Bowtie2 / Salmon / Kallisto) using MAGs as expression targets

Session 3

Fee: Rs 14800

Expression Quantification & Active Community Inference

From aligned reads to expression matrices

gene, ORF and KO level counts count tables and coverage mapping rate and QC metrics

Normalization and differential activity analysis

CPM, TPM and size factor ideas DESeq2 / edgeR style workflows multiple testing and effect sizes

Inferring active taxa, pathways and AMR expression

linking expression to taxonomic profiles DNA vs RNA ratios and activity scores expressed AMR and virulence signatures overview

Session 4

Fee: Rs 18800

Mini Capstone: Activity Profiles & Interpretation

Designing a small metatranscriptomic analysis

guided theory plus practical

From raw RNA reads to activity and differential expression tables

QC, depletion and mapping pipeline expression matrices and contrasts basic visualizations (heatmaps and volcano plots)

Deliverables: active community summary and short report

key active taxa and pathways table DNA vs RNA comparison figure narrative connecting activity to phenotype or environment

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Metatranscriptomics & Active Community Inference Training | RNA-Seq for Microbiomes & Activity Profiling

Metatranscriptomics & Active Community Inference — Hands-on