BIN310 Selected topics in genome analysis
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Showing course contents for the educational year 2016 - 2017 .
Course responsible: Lars Gustav Snipen
Teachers: Lars Gustav Snipen, Niklas Mähler
ECTS credits: 10
Faculty: Faculty of Chemistry, Biotechnology and Food Science
Teaching language: EN, NO
Limits of class size:
Teaching exam periods:
This course starts in Autumn parallel. This course has teaching/evaluation in Autumn parallel.
Course frequency: Odd years
First time: Study year 2006-2007
Modern sequencing technology shotgunand amplicon sequencing. Assmbly of genomes, RNAseq data and metagenomes. Sequence-variants (SNP-detection, orthologs, genotyping). Analyses based on whole-genome data. Metagenome studies and analyses of microbial communities. Even if most of the topics are related to microbiology most methods will have a more general nature.
KNOWLEDGE: Use of various sequencing technologies and know how we can get from reads to more informative sequences. Be able to sketch a selection of assembly algorithms. Have a good theoretical understanding of comparison and classification of sequences. Know some common statistical methods for association studies and use these on real data.
SKILLS: Students will be able to: Apply elements from the topics above to solve a project assignment in the course. Implementing the algorithms in R and use this scripting language for effective processing of large data sets. Present material both orally and in a written report.
Two lectures weekly. Two to four hours supervised solving of problems in the computer lab weekly. These hours can also to some degree be used for ad-hoc lectures on topics of special interest, if requested by the students. Oral presentation of written report.
Active use of Fronter.
Will be specified at the beginning of the course.
Introduction to bioinformatics equivalent to BIN210. Programming knowledge equivalent to INF120. Statistics equivalent to STAT200/STAT210.
Statistics equivalent to STAT300 or STAT310.
A written report on a topic announced at the start of the course. Oral presentation of the report.
Written exam, 3.5 hrs, counts 100%
Lectures: 26 hours. Exercises with instructor present: 44 hours. Individual study: 230 hours.
Special requirements in Science
Type of course:
Lectures: 2 hours per week. Computer lab exercises: 4 hours per week.
Students must bring their own laptop to computer-labs.
The exam will be approved by an external examiner. 25 selected exam papers will be evaluated by the external examiner.
Allowed examination aids: No calculator, no other aids
Examination details: Written exam: A - E / Ikke bestått