Lecture 8: RNA-sequence Analysis: Expression, Isoforms

RNA-seq principles

 - how can we characterize mRNA isoform expression using high throughput sequencing?

 

Differential expression and PCA

 - what genes are differentially expressed, and how can we characterize expressed genes?

 

Single cell RNA-seq

 - what are the benefits and challenges of working with single cells for RNA-seq? 

 

Two major approaches to RNA-seq analysis

1. Assemble read into transcripts. Typical issues with coverage and correctness.

2. Map reads to reference genome and identify isoforms using constrains.

 - Goal is to quantify isoforms and determine significance of differential expression

 - Common RNA-seq expression metrics are Reads per killobase per million reads (RPKM) or Fragments per killobase per reads (FPKM)

 

Scaling RNA-seq data (DEseq)

 

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