Analysis of Bulk RNAseq data - Extended Materials

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22nd - 28th July 2020: Zoom virtual school, University of Cambridge

Main Summer School page

These files contain some additional information and exercises not included during the taught course.

1. Obtaining public data
   • Downloading files from SRA and aligning
2. Raw read file format and QC
   • Introductory slides
   • Practical
   • Practical solutions
3. Raw read file format and QC
   • Example of using Trimmomatic to remove adapters
4. Short read alignment with HISAT2
   • Introductory slides
   • Practical
   • Practical solutions
5. QC of alignment
   • Introductory slides
   • Practical
   • Practical solutions
6. Pre-processing - extended
   • A brief intro to the tidyverse
   • A more extended tidyverse course can be found here: Introduction to R
7. Annotation and Visualisation - extended
   • Annotation with biomaRt
     • practical solutions
   • Additional annotation and plotting
8. Gene set testing - extended
   • Gene-set testing
   • practical solutions

Additional resources

Bioconductor help
Biostars
SEQanswers

Acknowledgements

This course is 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.