INF-BIO9121 – High Throughput Sequencing technologies and bioinformatics analysis
Course description
Course content
The course provides knowledge of high throughput sequencing technologies and hands-on experience with the analysis of data from various sequencing platforms and applications. Examples of applications that can be included are control of quantity and quality of data, analysis of small RNA sequencing data (miRNA) and transcriptome sequencing (mRNA-seq, cDNA), genome assembly, and SNP finding after resequencing (variant calling) . The course will introduce and use the command-line (unix), and the LifePortal (Uio’s Galaxy server) and the Genomic Hyperbrowser frameworks.
Learning outcome
After this course you will:
- understand the differences, benefits and drawbacks of the most current high throughput sequencing (HTS) technologies, and be able to decide which platform to use in what way for the different applications of HTS
- be confident in using the command-line (unix) for working with bioinformatics analysis of HTS data, and to evaluate the quantity- and quality of sequencing data in light of the intended analysis.
- be able to perform analysis, both on the command-line and through web-based frameworks, such as the Galaxy-based LifePortal framework at UiO, with data tailored towards different application, for example small RNA, transcriptome sequencing (RNA-seq), variant calling, genome assembly, statistical genomics, and others
- be able to critically evaluate, validate and judge the results of bioinformatics analysis of HTS experiments in terms of underlying assumptions, reliability, sensitivity and specificity, and evaluate their value for answering biological questions
- be able to report on bioinformatics analysis in such a way that the methods used and steps taken are transparent, thus enhancing reproducibility
- be aware of, and know to deal with, the ethical and data-sensitivity issues surrounding sequencing data derived from human subjects
Admission
PhD candidates from the University of Oslo should apply for classes and register for examinations through Studentweb.
If a course has limited intake capacity, priority will be given to PhD candidates who follow an individual education plan where this particular course is included. Some national researchers’ schools may have specific rules for ranking applicants for courses with limited intake capacity.
PhD candidates who have been admitted to another higher education institution must apply for a position as a visiting student within a given deadline.
A maximum of 30 students (INF-BIO5121 and INF-BIO9121 alltogether).
Ranking:
1) Phd students who have the course as mandatory
2) Others