Metatranscriptomics: Expression Dynamics in Microbiomes — Hands-on

Learn to profile active microbial functions via metatranscriptomics. This module covers experiment design and rRNA depletion, rigorous QC and host/contaminant removal, quantification with alignment-free and alignment-based approaches, normalization and differential expression suited for compositional RNA data, and interpretation across pathways, taxa, and time. Deliverables include reproducible notebooks, figures, and a mini report on a real dataset.

Metatranscriptomics: Expression Dynamics in Microbiomes

Help Desk · WhatsApp

Session Index

Session 1 — Design, rRNA Depletion & QC Session 2 — Mapping/Quant & Reference Strategies Session 3 — Normalization, DE & Time-Series Session 4 — Pathways, Integration & Reporting

Session 1

Fee: Rs 8800

Design, rRNA Depletion & QC

Study design & library prep

rRNA depletion (bacterial/archaeal/euk) strand-specific protocols ERCC spike-ins

Read intake & quality control

FastQC / MultiQC adapter/quality trimming (fastp) duplication/GC/5′–3′ bias

Host & rRNA removal

Bowtie2/KneadData (host) SortMeRNA/bbduk (rRNA) low-biomass safeguards

Session 2

Fee: Rs 11800

Mapping/Quant & Reference Strategies

Alignment-free quantification

Salmon / Kallisto txp→gene aggregation bias correction

Alignment-based workflows

HISAT2 / STAR (reference) featureCounts/HTSeq TPM/CPM interpretation

Reference choices (critical)

MAGs / metagenome gene catalogs UHGG/GTDB species sets de novo (rnaSPAdes/Trinity) overview

Session 3

Fee: Rs 14800

Normalization, DE & Time-Series Analytics

Normalization choices & caveats

TMM / DESeq2 size factors CLR/rCLR awareness spike-in scaling (ERCC)

Differential expression (community)

DESeq2 / edgeR / limma-voom covariates & batch effect sizes & FDR

Temporal & network analyses

trend/seasonality models WGCNA co-expression (overview) linking to taxa/ARGs

Session 4

Fee: Rs 18800

Pathways, Integration & Reproducible Reporting

Pathway & function interpretation

KO/EC/eggNOG regrouping MetaCyc/KEGG context link to HUMAnN outputs

Multi-omics integration

metagenome + transcriptome taxa-stratified expression case studies & dashboards

Reporting & deliverables

Quarto/R Markdown notebooks tables, volcano/heatmaps data dictionary & env files

PDF

Metatranscriptomics: Expression Dynamics in Microbiomes Training | rRNA Depletion, Salmon/Kallisto, DESeq2 & Pathways

Metatranscriptomics: Expression Dynamics in Microbiomes — Hands-on