The course is arranged as an intensive two-week course between October 8 and 19th at Department of Informatics, University of Oslo. The course is based on the contents of the previous courses entitled "Next-generation sequencing hands-on course", "Variant calling using High Through-put sequencing data" and "De novo genome assembly" courses. The content of the course has been further extended and updated. Hands-on exercises with real data will be a substantial part of the course.
The course is free of charge, and registration is required (15 participants in total). No accommodation or meals provided.
Prerequisites:
Since this is an introductory course, we do not require any prior knowledge in the subject. It is an advantage if the participants are able to install/compile programs and run simple commands using a terminal. We recommend a basic understanding of both bioinformatics and molecular biology, e.g. UiO courses INF4350 and MBV3070.
The course will cover the following topics:
- Introduction to various next-generation sequencing platforms and data formats;
- Introduction to Unix - commands and knowledge necessary to perform next-generation sequencing analyses;
- Quality control of sequence reads contained in a fastq file;
- de novo genome assembly of DNA-seq reads;
- Alignment of sequence reads to a reference genome using different state-of-the-art tools;
- Annotation of mapped sequence reads to coding regions;
- Statistical analysis of small RNA-seq and mRNA-seq;
- Assessing coverage of a capture experiment;
- Alignment refinement (duplicate removal, realignment, quality recalibration);
- Variant calling and annotation;
- Plotting and visualization of analysis-results;
- Basic use of Galaxy and the Genomic Hyperbrowser tools.
The course starts on Monday, October 8th at 9.30. Instruction and hands-on exercises are planned from 9.00 to 17.00 every day (from 9.30 to 17.00 on Mondays). Last day of teaching is Friday October 19th. Participants are expected to attend the complete the 2 weeks course. A detailed schedule will be provided later, in a follow-up e-mail addressed to all confirmed participants.
Teaching will take place in a computer lab with preinstalled computers. It is not necessary to bring a computer.
Applying
Registration is now closed.
In order to keep the course as interactive as possible, we will have to limit the number of participants. Therefore we ask each institution/group to only apply for one person.
To master/PhD students:
Please note that this course is now available as a university course from this autumn on at both master (INF-BIO5120) and PhD level (INF-BIO9120), in either case for 5 study points. Contact your study administration if you have more questions about how to register for the university course.
Please register to one of the following courses:
Phd course (5 study points) INF-BIO 9120.
Master level course (5 study points) INF-BIO5120.
NOTE that the deadline for registering to the course at UiO is 16th of August.