Environmental Metatranscriptomics, Nov 2018

These are the online materials for the environmental metatranscriptomics workshop run at CICESE in November 2018.

This workshop runs under a Code of Conduct. Please respect it and be excellent to each other!

Please use the following hackmd for notes: https://tinyurl.com/cicese-metaT

Day 1: Nov 8, 2018

Morning:

• Introduction and Metatranscriptomics overview
• Bienvenidos!
• Logging into the cluster
• Setting up the software
• Intro to TARA Oceans sample data
• Short read quality control

Lunch

Afternoon:

• Taxonomic classification with sourmash gather
• Sample Comparison
• Metatranscriptomic workflows and considerations

Day 2: Nov 9, 2018

Morning:

• Error Trimming
• Metatranscriptome Assembly with Megahit
• Assessing assembly quality
• Annotating your assembly
• Counting transcriptomes

Lunch

Afternoon:

• Filezilla
• Bioconda for software installation
• A brief discussion of workflows & repeatability

Additional Resources:

• Installing this software in the future
• References
• SEQ Answers
• Biostars
• Data Carpentry
• DIB Summer Institute

Suggested readings

• A global ocean atlas of eukaryotic genes - This is the paper from which we pulled all of our sample data.