INF-BIO9121 - High Throughput Sequencing technologies and bioinformatics analysis

Schedule, syllabus and examination date

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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

Prerequisites

Recommended previous knowledge

We recommend that students with a background in informatics have passed INF4350, and students with a background in biology or molecular biology have passed MBV3070.

Teaching

The course consists of five weeks, three days each week, of mostly practicals and some lectures. 1 to 2 weeks before these three weeks, there is a one-day introduction to the Unix command line, as a basic understanding of the unix shell is essential to follow the course. 80% attendance is required

Examination

Obligatory reports for the practical work performed each week, graded as pass/fail, at least 80% of reports must be passed

Home exam assignment judged by an oral examination of the home exam and a written report; and a written exam. Both exams have to be passed be passed in the same semester

The mandatory assignments must be approved prior to the exam and 80% attendance is required to take the final exam. The oral exam is held close to the written exam

Grading scale

Grades are awarded on a pass/fail scale. Read more about the grading system.

Explanations and appeals

Resit an examination

Students who can document a valid reason for absence from the regular examination are offered a postponed examination at the beginning of the next semester.

Re-scheduled examinations are not offered to students who withdraw during, or did not pass the original examination.

Withdrawal from an examination

It is possible to take the exam up to 3 times. If you withdraw from the exam after the deadline or during the exam, this will be counted as an examination attempt.

Special examination arrangements

Application form, deadline and requirements for special examination arrangements.

Facts about this course

Credits

10

Level

PhD

Teaching

Every autumn

Examination

Every autumn

Teaching language

English