Introduction to Bulk RNA-seq data analysis

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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:

Full RNAseq Analysis Course

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)
• DESeq2 - Ashley’s Script

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

• Bioconductor for relevant R packages
• DESeq2 Vignette
• RNAseq Workflow

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.

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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!