Webinar: New and Improved RNA-Seq Workflow

JULY 21, 2017     1 PM EDT, noon CDT, 11 AM MDT, 10 AM PDT

RNA-Seq data analysis has become vital to understanding gene structure and expression patterns in transcriptomic studies. A typical reference genome guided RNA-Seq workflow involves the following steps: quality control of reads, alignment of reads to reference genomes, assembly of reads, quantification, differential expression, and visualization. The current ecosystem of RNA-Seq tools and protocols is vast and diverse. The performance of these tools varies across computing platforms, and hence it becomes critical to choose an analysis protocol that is scalable and accurate when handling large datasets on different computing platforms.

In this webinar, we will demonstrate the updated Tuxedo protocols HISAT2, StringTie, and Ballgown, which align the sequencing reads to a reference genome determining its gene structure quality and differential gene expression patterns between experimental conditions. We will also demo another RNA-Seq quantification workflow, Kallisto and Sleuth, which relies on pseudo alignment of reads to a reference transcriptome. This second approach shows significant improvement in performance compared with the alignment-based methods in the first approach. This webinar will demo both workflows and the visualization of downstream results using CyVerse Cyberinfrastructure. The reference tutorials (not required for attendance) for this webinar are online at: https://wiki.cyverse.org/wiki/display/TUT/RNA-seq+Tutorial-+HISAT2%2C+St... and https://wiki.cyverse.org/wiki/display/TUT/RNA+seq+tutorials-+Kallisto+an....



Focus Forum webinars are offered on various topics and are designed to enhance users' experience with CyVerse tools and platforms. They give users an opportunity to interact with CyVerse staff and community members to learn about new tools, discuss "best practices" for performing analyses and troubleshooting any potential difficulties, and connect with the community. During the year, topics may focus on any CyVerse science area or service, or using and developing any platform. Users may suggest and vote for webinar topics through the Ask Forum.

Who Should Attend?

This webinar is open to people who are using the CyVerse resources and want to learn more about the specific topic. Users are encouraged to post questions and problems encountered to the Ask Forum for discussion during the webinar.

About the Presenter

Kapeel Chougule is a Computational Science Developer and CyVerse Bioinformatician at Cold Spring Harbor Laboratory. Kapeel earned his Master's degree in Bioinformatics from the University of Science in Philadelphia. He has broad bioinformatics experience with particular focus on Next Generation Sequencing application, especially RNA-seq and Genome annotation. His current interests include applying interactive visualization techniques for biological data interpretation and machine learning concepts in genomics. At CyVerse, Kapeel focuses on building tools and apps, providing Extended Collaborative Support (ECS), and helping teach new users how to use components of the CyVerse Cyberinfrastructure. Kapeel Chougule
Primary Contact: 

Tina Lee - CyVerse

End date: 
Friday, July 21, 2017 - 14:00