Overview

Instructor(s): Dr. Michael Dickens

Time: Friday, February 14, 2025 — 1:30PM-4:00PM CT

Location: Blocker 220

Prerequisite(s): Active HPRC account, basic Linux/Unix skills

This short course covers concepts of sequence mapping, variant calling and ChIP-seq analysis utilizing tools available on the HPRC clusters.

Course Materials

Presentation slides

The presentation slides are available as downloadable PDF files.

• Introduction to NGS (Spring 2025): PDF

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• Introduction to NGS (Fall 2024): PDF
• Introduction to NGS (Spring 2024): PDF
• Introduction to NGS (Fall 2023): PDF
• Introduction to NGS (Spring 2023): PDF
• Introduction to NGS (Fall 2022): PDF
• Introduction to NGS (Spring 2022): PDF
• Introduction to NGS (Fall 2021): PDF
• Introduction to NGS (Spring 2021): PDF
• Introduction to NGS (Fall 2020): PDF
• Introduction to NGS (Summer 2020): PDF
• Introduction to NGS (Spring 2020): PDF
• Introduction to NGS (Fall 2019): PDF
• Introduction to NGS (Spring 2019): PDF
• Introduction to NGS (Fall 2018): PDF
• Introduction to NGS (Spring 2018): PDF
• Introduction to NGS (Fall 2017): PDF
• Introduction to NGS (Spring 2017): PDF

Learning Objectives and Agenda

In this course, participants will learn:

• An overview of NGS Technology
• Sequence Quality Control (QC)
• How to find and use Template Job Scripts
• How to Visualize BAM Alignment Files
• Fundamentals of Sequence Variant Calling
• Fundamentals of RNA-seq and ChIP-seq
• How to use BioContainers

This course focuses, among others, on the following topics:

• NGS Technology
• NGS Tools on Grace
• Quality Control (QC)
• Template Job Scripts
• Visualize BAM Alignment Files
• Sequence Variant Calling
• RNA-seq
• ChIP-seq
• BioContainers

Note: During the class sessions many aspects of the material will be illustrated live via a login to Grace. Attendees will follow along and complete the exercises on their own laptops.

You are encouraged to contact the HPRC helpdesk with any questions regarding Grace.