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This hands-on, online course teaches data analysis for metatranscriptomics projects. It is aimed at those with little or no experience of using high performance computing (HPC) for data analysis. In the course we will cover: - navigating file directories and using the command line - logging into a remote cloud instance - using common commands and running analysis programs in the command line - what is metagenomics? - following a metatranscriptomics analysis workflow including:
- Perform quality control on RNA-seq reads
- Carry out adapter trimming and quality filtering
- Remove rRNA sequences from RNA-seq data
- Merge and prepare reads for downstream analyses
- Perform taxonomic profiling of metatranscriptomic data
- Functionally interpret expressed genes
- Visualise and explore results using interactive tools such as Krona
The course is taught as a mixture of live coding, online lectures, self-study and drop-in sessions.
## Prerequisites
This course assumes no prior experience with the tools covered in the workshop but learners are expected to have some familiarity with biological concepts, including the concept of genomes and microbiomes. Participants should bring their own laptops and plan to participate actively.
To get started, follow the directions in the Setup tab to get access to the required software and data for this workshop.
## Acknowledgments
The first two lessons are based on our [Prenomics](https://cloud-span.github.io/prenomics00-intro/) course; the rest are based on our [Metagenomics](https://cloud-span.github.io/metagenomics00-overview/) course.
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New repo for metatranscriptomics course. 🚧 WIP 🚧