Day 1 learning objectives

Today, we will introduce you to the first steps of analysing RNA sequencing (RNA-seq) data using the command line. We will learn about the pre-processing workflow we use to convert raw sequence reads to analysis-ready count data.

Introductory slides

Understand how RNA-seq data is generated
Review the applications of RNA-seq
Understand experimental design considerations for differential expression (DE) analysis
Understand the basic RNA-seq DE analysis workflow

Run the nf-core/rnaseq pipeline

Set up your computer for this workshop series
Log in to your Nimbus instance
Download the input data files
Run the nf-core/rnaseq command to excecute the pipeline

Why use nf-core workflows?

Understand why Nextflow and nf-core are good options for reproducible and portable bioinformatics workflows

The ins and outs of nf-core-rnaseq

Write and run a basic nf-core/rnaseq command to perform RNA-seq data pre-processing
Understand what input files and parameters are required to run the command
Review the output files generated by the nf-core/rnaseq pipeline
Understand how to adjust the run command to customise the workflow

The RNAseq pre-processing workflow

Understand the different steps in a typical RNA-seq pre-processing pipeline
Evaluate the results and outputs generated by the nf-core/rnaseq pipeline
Understand how to perform quality checking of raw sequence data
Understand the requirements for trimming raw RNA-seq reads
Understand the process of aligning RNA-seq reads to a reference genome
Understand how read alignments are converted to gene count data

All materials copyright Sydney Informatics Hub, University of Sydney