T. H. (Henry) Hung [email protected], University of Oxford

📬 For any intended reader only

<aside> 📢 Please don’t share this guide with anyone else without asking me first. Not because I want to keep this exclusive, but it contains information related to our departmental servers. Also the pipeline is not universal for all types of servers and projects and I can't hold accountability if someone uses this guide without consulting me.

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Introduction

RNA sequencing (RNA-seq) is a powerful tool to analyse the changing cellular transcriptome. One of the most common aims of RNA-seq is the profiling of gene expression by identifying genes (or subsequently, molecular pathways) that are differentially expressed (DE) between two or more biological conditions.

• Try clicking the triangle on the left

Pre-requisites

• What do I need to run this tutorial?

Tutorial

<aside> 🛠 This is still in development.

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🗄️ On a server

0-Setting up the environment

1-Quality controlling your reads

2-Pseudoaligning & quantifying transcript abundance