Informatics for RNA-Seq Analysis

Welcome

Welcome to Informatics for RNA-Seq Analysis 2018.

The course schedule can be found here.

Pre-readings, pre-work, and laptop setup instructions can be found here.

We are using Google Classroom for discussion. Join the Class at https://classroom.google.com, select the “+” symbol in the upper right corner, click on “Join Class” and enter the class code provided to you.

The full course notes are available as a single PDF.


Class Photo

Class Photo


Day 1

Day 1 and Day 2 refer to content in the RNA-Seq wiki.

Welcome

Ann Meyer

Introduction to Cloud Computing

Obi Griffith

Lecture

  • We have set up 30 instances on the Amazon cloud - one for each student. In order to log in to your instance, you will need a security certificate. If you plan on using Linux or Mac OS X, please download this certificate. Otherwise if you plan on using Windows (with Putty and Winscp), please download this certificate.

  • Detail instructions can be found here.

Module 1: Introduction to RNA Sequencing Analysis

Malachi Griffith

Lecture

Lab Practical

Lab practical

Installation

Reference Genomes

Annotations

Indexing

Data

Data QC

Module 2: RNA-seq Alignment and Visualization

Fouad Yousif

Lecture

Integrated Assignment

Hamza Farooq

Assignment Questions

Assignment Answers


Day 2

Module 2: RNA-seq Alignment and Visualization Lab Practical

Fouad Yousif

Lab Practical

Adapter Trim

Alignment

IGV

Alignment Visualization

Alignment QC

IGV Tutorial

Module 3: Expression and Differential Expression

Obi Griffith

Lecture

Module 3: Expression and Differential Expression Lab Practical

Lab Practical

Expression

Differential Expression

DE Visualization

Module 4: Reference Free Alignment

Malachi Griffith

Kallisto

Integrated Assignment

Assignment Questions

Assignment Answers

Keeping Up-to-date with RNA-Seq Analysis Developments

For additional resources, tutorials, future directions, and more please refer to the RNA-seq wiki


Day 3

Module 5: Genome Guided and Genome-Free Transcriptome Assembly

Brian Haas

Lecture

Bandage

Lab practical

Module 6: Functional Annotation and Analysis of Transcripts

Brian Haas

Lecture

Lab practical


Additional Optional Resources

Additional resources can be found on the RNA-Seq wiki.


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