Introduction to NGS Data Analysis Workshop¶
The University of Sydney, NSW - 27th - 29th June 2017
Instructors¶
- Katherine Champ (KC) - Bioplatforms Australia, Sydney
- Sonika Tyagi (ST) - AGRF, Melbourne
- Matthew Field (MF) - Australian National University/James Cook University, Cairns
- Xi (Sean) Li (SL) - Australian National University, Canberra
- Susan Corley (SC) - UNSW Systems Biology Initiative, Sydney
Timetable¶
Day 1 - Introduction to the command line, data quality & alignment & ChIP-Seq¶
27th June - Computer Lab 1.4, Charles Perkins Centre, University of Sydney, NSW
| Time | Topic | Links | Instructor |
|---|---|---|---|
| 09:00 | Introductions and course orientation | KC | |
| 09:45 | Practical: Introduction to the command line | MF | |
| 10:15 | Morning Tea | ||
| 10:40 | Practical: Introduction to the command line course and R course | MF | |
| 11:20 | Introduction to NGS- technology, data formats and introduction to quality control | MF | |
| 12:30 | Lunch | ||
| 13:15 | Quality control: Intro to practical | ST | |
| 13:25 | Practical: Quality control | ST | |
| 14:05 | Introduction to sequence alignment | SL | |
| 14:15 | Practical: Sequence alignment | SL | |
| 15:00 | Afternoon Tea | ||
| 15:25 | Introduction to ChIP-Seq | SL | |
| 15:55 | Practical: ChIP-Seq analysis - Peak calling and annotation | SL | |
| 16:30 | Q&A and day 1 wrap-up | All |
Day 2 - ChIP-Seq motif analysis and RNA-Seq analysis¶
28th June - Computer Lab 1.4, Charles Perkins Centre, University of Sydney, NSW
| Time | Topic | Links | Instructor |
|---|---|---|---|
| 09:00 | Practical: Motif analysis | SL | |
| 09:40 | Introduction to RNA-Seq | SC | |
| 10:30 | Morning Tea | ||
| 10:50 | Practical: Alignment and splice junction identification | SC | |
| 12:30 | Lunch | ||
| 13:30 | Practical: Differential gene expression with Bio-conductor package: EdgeR and Voom | SC | |
| 15:00 | Afternoon Tea | ||
| 15:30 | Practical: Biological interpretation | SC | |
| 16:30 | Q&A and day 2 wrap-up | All |
Day 3 - de novo Assembly¶
29th June - Computer Lab 1.4, Charles Perkins Centre, University of Sydney, NSW
| Time | Topic | Links | Instructor |
|---|---|---|---|
| 09:00 | Introduction to de novo assembly | ST | |
| 09:40 | Practical: de novo assembly using Illumina reads | ST | |
| 10:30 | Morning Tea | ||
| 10:50 | Practical: de novo assembly using Illumina reads (cont.) | ST | |
| 11:30 | Practical: de novo assembly using PacBio – Canu workflow | ST | |
| 12:30 | Lunch | ||
| 13:30 | Practical: de novo assembly using PacBio – Canu workflow (cont.) | ST | |
| 15:30 | Afternoon Tea | ||
| 15:50 | Practical: Polishing PacBio de novo assembly with Illumina reads | ST | |
| 16:30 | Q&A and workshop wrap-up | All | |
| 17:00 | Workshop Survey | KC |