Introduction to RNA-seq data analysis - Extended Materials

18th - 20th November 2020

Taught remotely

Bioinformatics Training, Craik-Marshall Building, Downing Site, University of Cambridge

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
   • Using Trimmomatic to remove adapter contamination from reads
3. Pre-processing - extended
   • A brief intro to the tidyverse
   • A more extended tidyverse course can be found here: Introduction to R
4. Annotation and Visualisation - extended
   • Annotation with biomaRt
     • practical solutions
   • Additional annotation and plotting
5. Gene set testing - extended
   • Gene-set testing
   • practical solutions

Source Materials for Practicals

The all of the lecture slides and other source materials, including R code and practical solutions, can be found in the course’s Github repository

Supplementary lessons

Introductory R materials:

• Introduction to R

Additional RNAseq materials:

Data: Example Mouse mammary data (fastq files): https://figshare.com/s/f5d63d8c265a05618137]

Additional resources - Places to get help

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.