RNA-seq-workshop

Refer to this page for workshop material https://genomicsaotearoa.github.io/RNA-seq-workshop/

This RNA-seq workshop aims to get you started with your own RNA-seq analysis and assumes you are already familiar with the basics of bash and R.

We will be using NeSI HPC for some of the analysis so make sure you have a NeSI account and you are able to login.

Go through the workshop prep files to ensure you are set to go: Prep_Files

Workshop outline (9:00am - 4:30pm)

• Overview of RNA-seq

• How to QC a fastq?

• How to trim a sequence file?

  • Quality trimming
  • Adaptor trimming

• How to align the sequencing reads on a reference using HISAT2

  • creating a reference sequence
  • aligning reads on a reference
  • Defining alignment format
  • Introduction to SAMtools

• How to get a count matrix

  • What is an annotation file
  • How to use featureCount

• Differential Gene Expression analysis

  • Using DESeq2, edgeR and Limma packages)

• Overrepresentation analysis (Gene Ontology)

• DISCUSSION AND FOLLOW-UP

Colaborative Document

Link

Post-Event Survey

Please take the survey to help us improve.

Attribution notice

• The material used to prepare for the workshop was extracted from Professor Mik Black's lectures for STAT435 at the University of Otago.

• Some code used in this workshop has been extracted from a collection of presentations, workshops and lectures by Prof. Thomas Girke, Institute for Integrative Genome Biology, UC Riverside: Link_1 and Link_2