Day 1

TimeDescriptionTopics coveredVideo lecturesComments
9:00 - 9:30
Grab some coffee and get settled in
9:30 - 11:15
Module 3
Read mapping with Kallisto (2 videos)
You will NOT have time to do the read mapping yourself. However, these two videos will give you clear instructions on HOW read alignment and 'pseudo alignment' work, and how you could do read mapping on your laptop with the workshop dataset on your own time. For the purposes of this workshop, you'll start your analysis using the outputs from Kallisto, which are already in your RStudio Cloud project
Coffee/stretch break
11:30 - 12:30
Module 4
Measuring gene expression; only watch Part 1 video
This lecture covers important concepts that are fundamental to understanding counts, RPKM/FPKM, TPM and normalization
12:30 - 1:30
Break for Lunch
1:30 - 2:15
Discussion + coding start
Importing Kallisto counts directly into R/bioconductor
This really the first place where you'll be working in the RStudio cloud project. I'll join you by Zoom to guide you through launching the project and running the code in the Step 1 script in order to get all the data imported into your R environment.
2:15 - 3:45
Module 6
Filtering and normalization (2 videos)
Start and finish the code in the Step 2 script
3:45 - 4:00
Coffee/stretch break
4:00 - 5:00
Module 7
Principal Component Analysis (PCA); only watch Part 1 video
Start and finish the code in the Step 3 script
5:00 - 6:00
Discussion and Day 1 wrap-up
We'll pick up with the PCA result and work together to plot the results, explore and discuss
A chance to review key concepts and to have a Q&A discussion