Offered by the ICBR Bioinformatics core, in collaboration with the UFHCC BQS SR and HSC Library.
Overview
This course consists of six lectures covering Next-Gen Sequencing data generation and computational analysis. Hands-on exercises will be performed on HiPerGator.
Registration Policy: there is no registration fee but please register by February 7th. You may attend selected lectures at your discretion.
This course is not for credit, but those who complete the course will receive a certificate.
Instructors
- Alberto Riva, ICBR Bioinformatics Core and UFHCC BQS SR (coordinator)
- Brad Barbazuk, ICBR Bioinformatics Core and UFHCC BQS SR
- Tongjun Gu, ICBR Bioinformatics Core and UFHCC BQS SR
- Rhonda Bacher, Dept of Biostatistics and UFHCC BQS SR
- Ana Conesa, Dept of Microbiology and Cell Science and UFHCC BQS SR
Syllabus
The course will take place in the HSC Library Computer Lab, room C1-121 (Communicore). All lectures are on Monday, 4-5:30pm. The lectures calendar is the following:
2/10/2020
- Introduction to Next-Gen Sequencing – High-throughput sequencing technologies, sample preparation, sequencing strategies.
- Slides: Sequencing Overview
- Instructors: BB
2/24/2020
- Introduction to HiPerGator – Basic shell commands, simple scripting, job submission.
- Slides: Basic Shell Commands
- Class Notes: Lecture 2 notes
- Instructors: AR, TG
3/9/2020
- Basic NGS analysis – Read cleanup and QC, alignment.
- Class Notes: Lecture 3
- Instructors: AR, TG
3/23/2020
- NGS analysis – RNA-Seq, ChIP-Seq, other applications.
- Instructors: AR, TG
3/30/2020
- Single-cell analysis – Technology overview, basic analysis, advanced applications.
- Instructor: RB
4/6/2020
- Advanced applications – Functional annotation of sequence data.
- Instructor: AC