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In this workshop, we will introduce analysis of RNA-seq data. This will include read alignment, quality control, quantification against a reference, reading the count data into R, performing differential expression analysis, and gene set testing, with a focus on the DESeq2 analysis workflow.
For the Makerere Summer School, we will only teach a small part of the full course as practicals. The full course can be found here:
- Introduction to RNAseq Data Preprocessing (lecture)
- Initial exploration of count data (lecture)
- Introduction to differential expression analysis (lecture)
- Differential Expression Analysis with DESeq2 (practical)
- DESeq2 - Ashley's Script
- Recap of Day 1
- Annotation and Visualistation (Slides)
- Annotation and Visualistation (Practical)
- Gene Set Testing (Slides)
- Gene Set Testing (Practical)
This course was based on the course RNAseq analysis in R prepared by Combine Australia and delivered on May 11/12th 2016 in Carlton. We are extremely grateful to the authors for making their materials available; Maria Doyle, Belinda Phipson, Matt Ritchie, Anna Trigos, Harriet Dashnow, Charity Law.
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The materials have been rewritten/modified/corrected/updated by various contributors over the past 8 years including:
Abigail Edwards Ashley D Sawle Chandra Chilamakuri Dominique-Laurent Couturier Guillermo Parada González Hugo Tavares Jon Price Mark Dunning Mark Fernandes Oscar Rueda Sankari Nagarajan Stephane Ballereau Tom Smith Zeynep Kalender Atak
Apologies if we have missed anyone!