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Informatics for RNA-Seq Analysis 2015

Workshop pages for students


Laptop Setup Instructions

Instructions for setting up your laptop can be found here: Laptop Setup Instructions

Pre-Workshop Tutorials

1) R Preparation tutorials: You are expected to have completed the following tutorials in R beforehand. The tutorial should be very accessible even if you have never used R before.

2) UNIX Preparation tutorials:

3) IGV Tutorial: Review how to use IGV Genome Browser if you have not used this tool before.


Pre-Workshop Readings

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

ENCODE RNA-Seq Standards

Methods to study splicing from high-throughput RNA sequencing data

Differential analysis of gene regulation at transcript resolution with RNA-seq

A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium

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


Logging into the Amazon cloud

Instructions can be found here.


R Review Session

RNA-seq2015_RReview.pdf
RNA-seq2015_RReviewScripts.R

Day 1


Welcome

*Faculty: Michelle Brazas*

Module 0: Introduction to cloud computing

*Faculty: Malachi and Obi Griffith*

Lecture slides:
RNASeq_Module0_AmazonPreTutorial.pdf RNASeq_Module0_AmazonPreTutorial.ppt](https://bioinformatics.ca/rnaseq2015module1pptx-0)
RNASeq_Module0_AmazonPreTutorial.mp4](https://bioinformatics.ca/rnaseq2015module1mp4)


Module 1: Introduction to RNA sequencing and analysis

*Faculty: Malachi Griffith*

Lecture slides:

RNASeq_Module1_Lecture.pdf
RNASeq_Module1_Lecture.ppt
RNASeq_Module1_Lecture.mp4

Lab introduction slides:

RNASeq_Module1_Tutorial.pdf

Lab practical:

http://www.rnaseq.wiki - Module 1 Tutorial


Module 2: RNA-seq alignment and visualization

*Faculty: Obi Griffith*

Lecture slides:

RNASeq_Module2_Lecture.pdf
RNASeq_Module2_Lecture.ppt
RNASeq_Module2_Lecture.mp4

Lab introduction slides:

RNASeq_Module2_Tutorial.pdf

Lab practical:

http://www.rnaseq.wiki - Module 2 Tutorial


Integrated Assignment - Day 1

*Faculty: Fouad Yousif*

Paper for Integrated Assignment:

Recurrent chimeric RNAs enriched in human prostate cancer identified by deep sequencing PMC3107329

Assignment Questions:

Integrated Assignment

Answer Key:

Integrated Assignment Answers


Day 2


Module 3: Expression and Differential Expression

*Faculty: Obi Griffith*

Lecture slides:

RNASeq_Module3_Lecture.pdf
RNASeq_Module3_Lecture.ppt
RNASeq_Module3_Lecture.mp4

Lab introduction slides:

RNASeq_Module3_Tutorial.pdf

Lab practical:

http://www.rnaseq.wiki - Module 3 Tutorial


Module 4: Isoform discovery and alternative expression

*Faculty: Malachi Griffith*

Lecture slides:

RNASeq_Module4_Lecture.pdf
RNASeq_Module4_Lecture.ppt
RNASeq_Module4_Lecture.mp4

Lab introduction slides:

RNASeq_Module4_Tutorial.pdf

Lab practical:

http://www.rnaseq.wiki - Module 4 Tutorial


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

For additional resources, tutorials, future directions, and more please refer to the RNA-seq wiki: http://www.rnaseq.wiki

Tools with installation instruction in our Amazon server

https://github.com/griffithlab/rnaseq_tutorial/wiki/Installation

Data Sets from Workshop

RNA-seq Integrated Data
RNA-seq Integrated Reference

Results from Instructor’s Instance on Amazon

RNA-seq result

Launching CBW AMI

Steps to launch CBW public AMI

  • AMI ID: ami-b9a253d2
  • AMI Name: CBW workshops 2015
View on GitHub