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
   • Introductory Slides
   • FastQC Practical (pdf)
     - FastQC Practical solutions (pdf)
   • Using Trimmomatic to remove adapter contamination from reads
3. Short read alignment with HISAT2
   • Introductory Slides
   • Alignment Practical (pdf)
     - Alignment Practical solutions (pdf)
4. QC of alignment
   • Introductory slides
   • Alignment QC Practical (pdf)
     - Alignment QC Practical solutions (pdf)
5. Gene expression quantification
   • Using Subread to count aligned reads - practical solutions
6. Data exploration - extended
   • A brief intro to the tidyverse
   • A more extended tidyverse course can be found here: Introduction to R
   • Further data exploration
7. 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!