Introduction to RNA-seq data analysis - Extended Materials

Taught remotely

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

Supplementary materials

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

1. Obtaining public data
   • Downloading files from SRA
2. Raw read file format and QC
   • Using Trimmomatic to remove adapter contamination from reads
3. Gene expression quantification
   • Using Subread to count aligned reads - practical solutions
4. Data exploration - extended
   • A brief intro to the tidyverse
   • A more extended tidyverse course can be found here: Introduction to R
   • Further data exploration
5. Annotation and Visualisation - extended
   • Annotation with biomaRt
     • practical solutions
   • Creating the annotation used in the course
   • Additional Visualisations

Supplementary lessons

Introductory R materials:

• Introduction to R

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.

The materials have been rewritten/modified/corrected/updated by various contributors over the past 5 years including:

Abigail Edwards Ashley D Sawle Chandra Chilamakuri Dominique-Laurent Couturier Guillermo Parada González Jon Price Mark Dunning Mark Fernandes Oscar Rueda Sankari Nagarajan Stephane Ballereau Zeynep Kalender Atak

Apologies if we have missed anyone!