15 Microbial metatranscriptomics (HT) data processing

Metatranscriptomics is a powerful tool for investigating gene expression patterns in complex microbial communities. It allows researchers to explore the functional diversity of microbial populations, providing insights into the metabolic pathways and interactions that drive community dynamics. The analysis of microbial metatranscriptomic data can be conducted following two main strategies, which depend on whether a reference catalogue of annotated bacterial genomes is available or not.

In the following two chapters, you will find example pipelines to process microbial metatranscriptomic data through both strategies: