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 your current analysis pipeline into a makefile structure. When complete, you should be able to run the current analysis with make all.