Introduction to Bulk RNA-seq data analysis
Outline
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:
Day 1 (Thursday 21st September)
- Introduction to RNAseq Data Preprocessing (lecture)
- Initial exploration of count data (lecture)
- Introduction to differential expression analysis (lecture)
- Differential Expression Analysis with DESeq2 (practical)
Day 2 (Friday 22nd September)
- Recap of Day 1
- Annotation and Visualistation (Slides)
- Annotation and Visualistation (Practical)
- Gene Set Testing (Slides)
- Gene Set Testing (Practical)
Additional Resources
Acknowledgements
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.
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!