Introduction to RNA-seq data analysis - Extended Materials

19th - 21st May 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.

Day 1

1. Raw read file format and QC
   • Example of using Trimmomatic to remove adapters
2. Quantification with SubRead
   • Practical
   • Practical solutions

Day 2

1. RNA-seq Pre-processing

   • Practical solutions

Day 3

1. Annotation and Visualisation of RNA-seq results

   • practical solutions

2. 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:

• Downloading files from SRA and aligning
• Additional annotation and plotting

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

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.