Date:Monday 18 - Wednesday 20 March 2019
Venue:LANGEBIO, Cinvestav - LANGEBIO, Cinvestav Libramiento Norte Carretera Leon Km 9.6, Irapuato, GUA, 36821, Mexico
Application opens:Friday 14 December 2018
Application deadline:Sunday 03 February 2019
Participation:Open application with selection
Registration fee:$700 MXN
This course will provide an introduction to the technology, data analysis, tools and resources for next generation sequencing (NGS) data.
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. The course content makes use of data derived mainly from eukaryotic non-model organisms in a biodiversity context.
This course is suitable for postgraduate wet-lab researchers at any career stage within Latin America who are working with and/or generating their own transcriptomic datasets.
Participants will require a basic knowledge of the Unix command line and the R statistical package. We recommend these free tutorials:
- Basic introduction to the Unix environment: www.ee.surrey.ac.uk/Teaching/Unix
- Introduction and exercises for Bio-Linux 7: http://nebc.nerc.ac.uk/support/training/course-notes/past-notes/intro-bl7
- Basic R concept tutorials: www.r-tutor.com/r-introduction
Participants without basic knowledge of these resources will have difficulty in completing the practical sessions. We strongly recommend that you make every effort to access these materials and other training available online or within your host institute to best prepare you for the course.
A number of travel fellowships are available for this course - early-stage researchers and researchers from underrepresented groups are especially encouraged to apply for CABANA travel fellowships. You can apply for travel fellowships via the course application form.
After this course you should be able to:
- Describe NGS and its applications in biological research
- Perform read alignments
- Assemble transcriptomes
- Perform differential gene expression analysis and visualize results in R and ggplot2
- View and explore data using Ensembl genome browser
Day 1 – Monday 18 Mar 2019
|09:20-10:30||Introduction to high-throughput (NGS) sequencing technologies and applications (lecture)||Selene Fernandez|
|11:00-13:00||Introduction to the fastq format and quality control of NGS data (lecture + prac)||Selene Fernandez|
|14:00-15:00||Read alignment (lecture)||Selene Fernandez|
|15:20-17:00||Read alignment (practical)||Selene Fernandez|
Day 2 – Tuesday 19 March 2019
|09:00-10:30||Genome guided transcriptome assembly (lecture + practical)||Selene Fernandez|
|11:00-13:00||Genome guided transcriptome assembly (practical continued)||Selene Fernandez|
|14:00-16:00||Differential gene expression analysis (lecture + practical)||Selene Fernandez|
|16:00-17:00||Keynote lecture||Peter Stadler|
|18:00-20:00||Social event (Faculty club)|
Day 3 – Wednesday 20 March 2019
|09:00-10:30||Ensembl Genome browser (webinar)||Erin Haskell|
|11:00-12:00||Ensembl Genome browser (webinar)||Erin Haskell|
|12:00-13:00||Exploring differential expression results in R (ggplot2 practical)||Selene Fernandez / Cei Abreu|
|14:00-15:00||Exploring differential expression results in R (ggplot2 practical)||Selene Fernandez / Cei Abreu|
|15:20-17:00||Exploring differential expression results in R (ggplot2 practical)||Selene Fernandez / Cei Abreu|
|17:00-17:30||Course close and feedback||Selene Fernandez|