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Day 9: RNA-Seq I, Introduction to RNA-Seq

Day 9: RNA-Seq I, Introduction to RNA-Seq Short-Read Workshop 2017

Welcome to Day 9 of the Short-Read Sequencing Analysis Workshop. This year we have split up the RNA-Seq analysis portion into 2 days. This first day we will focus on the different kinds or RNA-Seq experiments, considerations for library prep, and the theory behind mapping spliced RNA-seq reads and determining expression levels. The in-class portion will be spent performing read mapping for a human RNA-Seq data set, visualization of the data, and creating a counts table for expression levels over each gene/transcript. The second day will be spent focusing on differential expression analysis.

 

Videos for Day 9 and 10

9.1 RNA Sequencing Introduction

9.2 Mapping RNA Seq Data

9.3 Running Tophat2

9.4 Intro to DEv2

9.5 Differential Expression with DESeq

9.6 Cufflinks

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