EMBL-EBI Workshop: Analysis of genome scale data from bulk and single-cell sequencing
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Date:
Monday 19 - Friday 23 November 2018Venue:
NIBMG - National Institute of Biomedical Genomics, University Of Kalyani, Kalyani, West Bengal, 741251, IndiaApplication opens:
Thursday 12 July 2018Application deadline:
Monday 15 October 2018Participation:
Open application with selectionContact:
Partha P. MajumderRegistration fee:
£0Registration closed
Course Overview
This course will provide practical training to researchers in India who are engaged in research or applications that involve analyses of data generated by massively-parallel DNA sequencers using DNA isolated from bulk cells or a single-cell. This course will provide an introduction to the technology, data analysis, and key bioinformatics tools and databases. The content is intended to provide a broad overview of the subject areas, and to highlight key resources, approaches and methodologies. Topics will be delivered using a mixture of lectures, practical sessions and open discussions. Practical work during the course will use small, example data-sets and there will not be scope to analyse personal data.
Audience
This course is open to all scientists and application specialists who are engaged in genome-scale research. Preference will be given to junior-level scientists who can in turn train others in their institutions.
No knowledge of programming is required, but an undergraduate level knowledge of biology is required.
Modules
- ensemblensembl-genomes
- expression-atlas-gene-expression-across-species-and-biological-conditions
Learning outcomes
After this course you should be able to:
- Use basic statistics, UNIX and R commands to navigate the command line, employ and interpret statistics from NGS data.
- Use a range of bioinformatics software and tools to undertake basic analysis of NGS data
- State the advantages and limitations of NGS analyses
- Apply various CNV detection methods
- Submit, browse and access a range of NGS data available in public repositories using EBI resources
Programme
Day 1 – Monday 19 November |
||
|---|---|---|
| 08:30 - 08:40 | Welcome | Partha Majumder |
| 08:40 - 09:35 | Introductions and networking | Cath Brooksbank |
| 09:35 - 09:45 | Gratitude | Partha Majumder |
| 09:45-10:00 | Break | |
| 10:00-11:00 | Statistics: Probability, Distributions, Tests of significance | Partha Majumder |
| 11:00-13:00 | Overview of NGS Technologies: Platforms, Chemistry, library preparation | Arindam Maitra |
| 13:00-14:00 | Lunch | |
| 14:00-15:30 | Introduction to EMBL-EBI Resources | Cath Brooksbank, Astrid Gall, Laura Huerta |
| 15:30-17:00 | Introduction to ENA and NGS Workflows | Sam Holt (webinar) |
| 17:00-17:30 | Break | |
| 17:30-19:30 | Introduction to Ensembl | Astrid Gall |
| 19:30 | End of Day 1 | |
Day 2 – Tuesday 20 November |
||
|---|---|---|
| 08:30-10:15 | Introduction to NGS Data Analysis | Nidhan Biswas |
| 10:15-10:30 | Break | |
| 10:30-12:30 | Linux: Introduction to the Command Line | Nidhan Biswas |
| 12:30-13:30 | Lunch | |
| 13:30-15:00 | Introduction to NGS file formats, databases and associated tools | Chitrarpita Das |
| 15:00-15:30 | NGS Data QC | Swati Jaiswal |
| 15:30-16:30 | Exome Sequence data analysis: Alignment, Read Filtering, Variant Calling | Nidhan Biswas |
| 16:30-17:00 | Variant annotation and Variant Filtration | Nidhan Biswas |
| 17:00-17:15 | Break | |
| 17:15-18:15 | Introduction to R: Commands & Functions | Saroj Mohapatra |
| 18:15-19:00 | Case Study: Data Processing through R | Saroj Mohapatra |
| 19:00 | End of Day 2 | |
Day 3 – Wednesday 21 November |
||
| 08:30-09:30 | Read and Mutation Visualization through IGV | Arnab Ghosh |
| 09:30-10:30 | Read Visualization in Ensembl | Astrid Gall |
| 10:30-10:45 | Break | |
| 10:45-11:30 | Analysis of Genome Structural Alterations: CNV & SV | Chitrarpati Das |
| 11:30-12:30 | CNV Detection from Genome-WIde Array Data | Nidhan Biswas & Chitrarpati Das |
| 12:30-13:00 | CNV Detection from Sequence Data: Paired-end and Mate-pair | Nidhan Biswas & Chitrapati Das |
| 13:00-14:00 | Lunch | |
| 14:00-16:00 | Ensembl workshop - Variation / VEP | Astrid Gall |
| 16:00-16:30 | Introduction to DGVa for CNV Data | Baron Koylass (webinar) |
| 16:30-17:00 | Break | |
| 17:00-18:30 | Ensembl workshop - Regulation | Astrid Gall |
| 19:00 | Special dinner | |
Day 4 – Thursday 22 November |
||
| 08:30-09:30 | Ensembl workshop - Comparative Genomics | Astrid Gall |
| 09:30-10:30 | Ensembl workshop - Biomart (Data export tool) | Astrid Gall |
| 10:30-10:45 | Break | |
| 10:45-11:15 | Targeted Sequencing and its application | Arindam Maitra |
| 11:15-11:45 | RNA-Seq: libraries to data generation | Arindam Maitra |
| 11:45-13:00 | Bulk RNA sequencing | Analabha Basu |
| 13:00-14:00 | Lunch | |
| 14:00-15:45 | Bulk RNA sequencing practical | Debodipta Das & Shatakshee Chatterjee |
| 15:45-16:45 | Circos - Mutation and CNV Visualization | Arnab Ghosh |
| 16:45-17:00 | Break | |
| 17:00-18:00 | Introduction to EVA | Baron Koylass (webinar) |
| 18:00-19:00 | COSMIC data resource for cancer mutations | Simon Forbes & Nidhi Bindal(webinar) |
| 19:00 | End of day 4 | |
Day 5 – Friday 23 November |
||
| 08:30-10:30 | Transcriptomic data resources and tools | Laura Huerta |
| 10:30-11:00 | Break | |
| 11:00-12:30 | Transcriptomic data resources and tools | Laura Huerta |
| 12:30-13:30 | Lunch | |
| 13:30-14:30 | Single-cell RNA sequencing and the Human Cell Atlas | Laura Huerta & Dani Welter (webinar) |
| 14:30-16:00 | Single cell RNA sequencing: Methods | Arindam Maitra |
| 16:00-17:00 | Single cell RNA sequencing: Analysis approaches and considerations | Nidhan Biswas |
| 17:00-17:15 | Break | |
| 17:15-17:45 | Data integration challenges and solutions | Partha Majumder |
| 17:45-18:00 | Wrap-up and feedback | |