Overview

Instructor: Michael Dickens

Time: Friday, February 23, 2024 — 10:00AM-12:30PM CT

Location: Blocker 220

Prerequisites: Current HPRC account

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 2024): PDF

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• 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

Agenda

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. They will need to configure their laptops to use the TAMULink wireless network. Relevant details on this can be found at: http://tamulink.tamu.edu

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