Image credit: 'Abacus' ca. 1946: textile, Paul Rand

Lecture slides

Homework: Introduction to the Tidyverse (~4hrs) - due before the start of class on March 6th.

Overview

Now that we’ve aligned our reads, it’s time to discuss units for measuring gene expression. We’ll discuss differences between RPKM and TPM, and how these units relate to basic properties of your reference file and data. We’ll also discuss normalization within and between samples. To conclude this class, we’ll fire up RStudio and take a look at our first script.

Goals

  • Review steps from last class (using Kallisto).
  • Discuss output from Kallisto and units of measurement for RNAseq and ‘normalization’
  • Open and discuss our first script, including installation of packages
  • Begin to discuss annotations (time permitting)

Code

Step 1 script

Reading

What the FPKM? - Blog post by Harold Pimentel discussing within sample normalization and the meaning of RNAseq expression units

Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples. Theory in Biosciences, Dec 2012

Between sample normalization in RNAseq - another great blog post from Harold Pimentel on between-sample normalization.