Introduction to Next Generation Sequencing Analysis

Overview

Instructor: Michael Dickens

Time: Friday, April 2, 10:00AM-12:30PM

Location: Zoom session only

Prerequisites: None

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

Course Materials

Presentation slides

The presentation slides are available as downloadable PDF files.

  • 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 Tools
  • NGS sequencing overview
  • FASTQ Quality Control
  • Aligning Sequences to a Reference Genome
  • Sequencing Error Correction
  • Sequence Alignment Visualization
  • Variant Calling (SNPs, indels)
  • Variant Annotation
  • ChIP-seq overview
  • Biocontainers

Note: During the class sessions many aspects of the material will be illustrated live via a login to Terra. Attendees are welcome to follow these parts with 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 Terra.