Informatics for RNA-Seq Analysis 2019
Welcome
Welcome to Informatics for RNA-Seq Analysis 2019.
The course schedule can be found here.
Meet your faculty here
We are using Slack for discussion. Join the Slack channel.
CLASS MATERIALS: The full course notes are available as a single PDF.
Pre-Workshop Preparation
Laptop Setup Instructions
Instructions to setup your laptop can be found here.
Pre-workshop Tutorials
Pre-readings and pre-work can be found here here.
It is in your best interest to complete these before the workshop.
Class Photo
Day 1
Day 1 and Day 2 refer to content on rnabio.org.
Welcome
Michelle Brazas
Module 1: Introduction to Cloud Computing
Malachi Griffith
Updated Lecture on Connecting to AWS
Lab Practical: Connecting to the Cloud
- We have set up instances on the Amazon cloud - one for each student. In order to log in to your instance, you will need a security certificate. The certificates will be uploaded to Slack. If you plan on using Linux or Mac OS X, Please use CBWRNA.pem; Otherwise if you plan on using Windows (with Putty), please use CBWRNA.ppk.
You can also download from here. Mac/Linux certificate, Windows certificate.
Module 2: Introduction to RNA Sequencing Analysis
Malachi Griffith
Module 2 Lab Practical
Module 3: RNA-seq Alignment and Visualization
Malachi Griffith
Module 3: RNA-seq Alignment and Visualization Lab Practical
Malachi Griffith
Integrated Assignment
Megan Richters and Kelsy Cotto
Day 2
Module 4: Expression and Differential Expression
Obi Griffith
Updated Lecture 4-PartA
Updated Lecture 4-PartB
Updated Lecture 4-PartC
Module 4 Lab
Module 5: Reference Free Alignment
Obi Griffith
Module 6: Isoform Discovery and Alternative Expression
Obi Griffith
Integrated Assignment
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 7: Genome Guided and Genome-Free Transcriptome Assembly
Brian Haas
Module 8: Functional Annotation and Analysis of Transcripts
Brian Haas
Post Workshop
Post workshop content for data sets, AWS image, tools and install instructions can be found here
Additional Optional Resources
Additional resources can be found on the RNA-Seq wiki.
Thank you for attending the Informatics for RNA-Seq Analysis workshop! Help us make this workshop better by filling out our survey