Informatics for RNA-Seq Analysis

Welcome

Welcome to Informatics for RNA-Seq Analysis 2017.

The course schedule can be found here.

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

If you have questions or comments, visit the workshop Q&A forum.


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), please download this certificate.

  • Detail instructions can be found here.

Module 1: Introduction to RNA Sequencing Analysis

Malachi Griffith

Lecture

Recording

Lab Practical

Lab practical

Installation

Reference Genomes

Annotations

Indexing

Data

Data QC

Module 2: RNA-seq Alignment and Visualization

Fouad Yousif

Lecture

Recording

Lab Practical

Lab Practical

Adapter Trim

Alignment

IGV

Alignment Visualization

Alignment QC

Integrated Assignment

Fouad Yousif

Paper: Recurrent chimeric RNAs enriched in human prostate cancer identified by deep sequencing

Assignment Questions

Assignment Answers


Day 2

Module 3: Expression and Differential Expression

Obi Griffith

Lecture

Recording

Lab Practical

Lab Practical

Expression

Differential Expression

DE Visualization

Module 4: Reference Free Alignment

Malachi Griffith

Kallisto

Module 5: Isoform Discovery and Alternative Expression

Malachi Griffith

Lecture

Recording

Lab Practical

Lab Practical

Ref Guided

De novo

Merging

Differential Splicing

Splicing Visualization

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 6: Genome-Free De Novo Transcriptome Assembly

Brian Haas

Lecture

Recording

Bandage

Lab practical

Module 7: Functional Annotation and Analysis of Transcripts

Brian Haas

Lecture

Recording

Lab practical


Thank you for attending the Informatics and RNA-Seq Analysis workshop! Help us make this workshop better by filling out our survey