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Overview

Learning Objectives

By the end of this week, students will be able to:

  • Describe the concept of 'looping' to iterate commands over multiple items
  • Automate a task by using a loop inside of a shell script
  • Understand applications of RNA sequencing
  • Introduce the overall differential expression workflow
  • Understand experimental design concepts such as replicates and batch effects
  • Understand different types of library preps, their requirements and uses.
  • Understand the types of data that is accessible from Gene Expression Omnibus (GEO)
  • Use the command-line interface to copy over data from GEO
  • How to submit a job using SLURM