Next Generation Sequencing Data Analysis Workshop
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Date:
Tuesday 16 - Friday 19 September 2014Venue:
Rajiv Gandhi Centre for Biotechnology (RGCB) - Thycaud PO, Thiruvananthapuram, Kerala, 695014, IndiaApplication opens:
Tuesday 01 July 2014Application deadline:
Saturday 16 August 2014Participation:
Open application with selectionContact:
Frank O’DonnellRegistration fee:
Rs.30,000Registration closed
Course Overview
The four-day hands-on residential training course organized by RGCB and EBI will include classroom presentations and extensive hands-on practical sessions using complete data sets. This course is designed to introduce bioinformatics tools available for analysis of Next Generation Sequencing (NGS) to individuals who have a basic background in Bioinformatics or Genomics. Hands-on exercises will be performed with Linux command-line.
Audience
This workshop is for early career scientists, post doctoral fellows and senior PhD students working in the areas of cancer genomics and bioinformatics. Participants will require basic knowledge of Unix commands, Bio-linux 7 and the R statistical package.
Learning outcomes
After this course you should be able to:
- Process your NGS data to remove low quality sequences
- Discuss NGS workflows for ChIP-Seq and RNA-seq
- Submit your data to public repositories
Programme
| Time | Topic | Trainer |
|---|---|---|
| Day 1 - Introduction to NGS analysis, Quality Control and Mapping | ||
| 9:00 - 9:30 | Welcome and Introduction to the course | RGCB and EBI |
| 9:30 - 10:30 | Introduction to Linux, R and Bioconductor | Bijesh G and Reshmi Girija-Devi |
| 10:30 - 11:00 | Coffee / Tea | |
| 11:00 - 12:30 | Introduction to Linux, R and Bioconductor (Cotd) | Bijesh G and Reshmi Girija-Devi |
| 12:30 - 13:00 | Introduction to EBI | Rajesh Radhakrishnan |
| 13:00 - 14:00 | Lunch | |
| 14:00 - 15:00 | Next Generation sequencing overview | Maria Xenophontos |
| 15:00 - 15:30 | Tools and output formats | Nils Kölling |
| 15:30 - 16:00 | Coffee / Tea | |
| 16:00 - 17:00 | Tools and output formats | Nils Kölling |
| 17:00 - 17:30 | NGS quality control | Maria Xenophontos / Nils Kölling |
| 17:30 - 18:00 | Q/A and Wrap Up | All |
| 19:00 - | Dinner | |
| Day 2 - ChIP-Seq analysis | ||
| 9:00 - 10:30 | Introduction to ChIP-seq | Maria Xenophontos |
| 10:30 - 11:00 | Coffee / Tea | |
| 11:00 - 12:00 | Sequence alignment | Nils Kölling / Maria Xenophontos |
| 12:00 -13:00 | ChIP-seq - peak calling and annotation | Nils Kölling / Maria Xenophontos |
| 13:00 - 14:00 | Lunch | |
| 14:00 - 14:30 | ChIP-seq - peak calling and annotation (Cotd) | Nils Kölling / Maria Xenophontos |
| 14:30 - 15:30 | ChIP-seq - motif analysis | Nils Kölling / Maria Xenophontos |
| 15:30 - 16:00 | Coffee / Tea | |
| 16:00 - 16:30 | ChIP-seq - enrichment plots | Nils Kölling / Maria Xenophontos |
| 16:30 - 17:30 | Gene Regulation | Nils Kölling / Maria Xenophontos |
| 17:30 - 18:00 | Q/A | All |
| 19:00 - | Dinner | |
| Day 3 - RNA-Seq analysis | ||
| 9:00 - 10:30 | Introduction to RNA-seq | Nils Kölling / Maria Xenophontos |
| 10:30 - 11:00 | Coffee / Tea | |
| 11:00 - 12:00 | RNA-seq - Alignment and splice junction identification | Nils Kölling / Maria Xenophontos |
| 12:00 - 13:00 | RNA-seq - Transcriptome assembly | Nils Kölling / Maria Xenophontos |
| 13:00 - 14:00 | Lunch | |
| 14:00 - 15:00 | RNA-seq analysis - Differential expression analysis | Nils Kölling / Maria Xenophontos |
| 15:00 - 15:30 | RNA-seq - Functional annotation | Nils Kölling / Maria Xenophontos |
| 15:30 - 16:00 | Coffee / Tea | |
| 16:00 - 16:30 | RNA-seq - Functional annotation (Cotd) | Nils Kölling / Maria Xenophontos |
| 16:30 - 17:30 | RNA-seq - Advanced differential expression | Nils Kölling / Maria Xenophontos |
| 17:30 - 18:00 | Q/A | All |
| 19:00 - | Dinner | |
| Day 4 - Introduction to European Nucleotide Archive (ENA) | ||
| 9:00 - 10:00 | Introduction to ENA | Rajesh Radhakrishnan |
| 10:00 - 10:30 | NGS Read submissions and archiving | Rajesh Radhakrishnan |
| 10:30 - 11:00 | Coffee / Tea | |
| 11:00 - 11:30 | NGS Read submissions and archiving | Rajesh Radhakrishnan |
| 11:30 - 12:30 | NGS Read exploring | Rajesh Radhakrishnan |
| 12:30 - 13:00 | Brief introduction to EBI metagenomics | Rajesh Radhakrishnan |
| 13:00 - 14:00 | Lunch | |
| 14:00 - 14:30 | NGS data compression and introduction to CRAM | Vadim Zalunin |
| 14:30 - 15:30 | CRAM | Vadim Zalunin |
| 15:30 - 16:00 | Coffee / Tea | |
| 16:00 - 16:30 | CRAM | Vadim Zalunin and Rajesh Radhakrishnan |
| 16:30 - 17:00 | Discussion and Debate - Q/A | All |
| 17:30 - 18:00 | End of course and online feedback form | All |
| 19:00 - | Dinner | |