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Citation reference (copy and paste into your CV): 

"Whole exome sequencing analysis in Ruddle Cluster". (November 17th, 2022). 2 hours workshop, Bioinformatics Support Hub, Cushing/Whitney Medical Library, Yale School of Medicine.  https://guides.library.yale.edu/WES_p2p 

Workshop Summary:

This workshop was part of the third season of the Peer-to-Peer Teaching sessions. These are taught by our own community members to fill knowledge gaps and keep up with the accelerated pace at which bioinformatics grows. This season we are pleased to announce sessions covering * Image analysis methodologies (imageJ and QuPath) * Omics analysis in R and/or Python * Biomedical Data analysis using the clusters * Statistical analysis software (Prism) *Science communication (Illustrator).

This session on "Whole exome sequencing analysis in Ruddle Cluster" was designed and delivered by Mar Giner-Calabuig, PhD, from the Department of Medicine (Digestive Diseases).

Summary: 

Whole exome sequencing is a technique for sequencing all protein-coding genes in a genome. A typical workflow of WES analysis includes sequence alignment, variant calling, variant filtering and annotation. In this demonstration you learned how to perform all the above-mentioned steps, using an in-house pipeline in ruddle. Ruddle is one of the Yale computers clusters. Because the clusters run on the Linux operating system, we covered the basic Linux commands to interact with the cluster.

This workshop covered: 

• Locate, move and execute files in the clusters using basic Linux commands.
• Transfer files between ruddle and your local machine
• Request a working node
• Access the Sequencing Data
• Analyze WES data in ruddle using James Knight’s pipeline

Duration: 2 hrs

Instructor: Mar Giner-Calabuig, PhD