QC & Preprocessing
A metatranscriptome is the collection of RNA transcripts produced by the microorganisms coexisting in a sample at a given moment. Unlike metagenomics, which provides information about the potential genetic capabilities of a community, metatranscriptomics captures the active functional processes, revealing which genes are being expressed and under what conditions.
In this lesson, we will discuss how to define metatranscriptomics and explore the challenges associated with analyzing RNA from complex microbial communities. We will also outline a typical workflow for metatranscriptomics analysis, including steps for processing, quantifying, and interpreting community-wide gene expression data.
We will then log into our cloud instance and take a look at some data. Then, we’ll go through the first two steps in our workflow: quality control and metagenome assembly.
By the end of this lesson you will be able to:
- explain what metatranscriptomics is and the challenges of working with RNA from complex microbial communities
- assess raw sequencing read quality using FastQC
- trim adapters and low-quality bases from RNA-seq reads using Cutadapt
- remove ribosomal RNA sequences to enrich for messenger RNA (mRNA) using SortmeRNA
You should be aware that some of the analyses in this lesson can take several hours to run - these will be completed outside of the taught lesson. You will receive guidance about this from your course instructors.