README.md

Introduction

This week we will look at the salmon RNA-Seq quantification tool. It uses a psuedo-mapping technique to rapidly quantify transcriptomic data. In addition to learning the salmon tool we will cover makefiles. These types of files are an important piece of a bioinformatics toolbox because they can encapsulate complex pipelines in a single file.

Learning Objectives

By the end of this week you should be able to:

• Recite and describe the three steps of a salmon quantification pipeline.
• Construct commands for building salmon indexes, quantification, and merging.
• Run make commands.
• Describe makefile replacements.
• Utilize wildcard and patsubst makefile functions to create file-conditional makefile pipelines.

Assignment

Adjust the makefile to run on the full or mini directory. Then, create the gene expression matrix for each grouping and place them in your exercises folder with a Readme describing the changes you made.