790379 Using bioinformatics for expression profiling by next generation sequencing

Type
Lecture and exercise
Semester hours
2
Lecturer (assistant)
Labaj, Pawel
Organisation
Offered in
Wintersemester 2024/25
Languages of instruction
Englisch
Content

We will cover the following topics:
- Next Generation Sequencing (NGS): theory and application
- NGS for gene/transcript expression profiling: RNA-Seq protocols and data-processing
- The power and limitations of RNA-seq: Complementarity with expression profiling by microarrays
- Characterizing NGS technology, consequences of RNA-seq theory for understanding results
- Comparing approaches to analysis: current technical developments and challenges
- Signal-level data RNA-Seq processing to applications and interpretation of results

The course is held in English.

We look forward to seeing you!
Previous knowledge expected

A familiarity with computer based methods and concepts of data analysis is highly
recommended (eg. by completion of 791330)
Objective (expected results of study and acquired competences)

IStudent will be able to describe the process of the gene/transcript expression profling by the sequncing technology, its evolution (towards NGS) and application. Student will be able to list the up to date RNA-Seq protocols and data-processing approaches.
Student will be able to compare the expression profiling technologies (RNA-Seq and microarrays) and identify power and limitations of each of them. Student thus will be able to identify recommended application scenarios for both technologies.
Student will know how to apply the state of the art academic software (command line as well as in the R environment) for RNA-Seq data processing. Will also know how to apply appropriate software for downstream analysis.
Student will be able to compare different approaches for RNA-Seq data analysis based on the current technical developments. Will also be able to identify the challenges in the field.
Based on the performed analysis student will be able to characterize the NGS technology and explain the obtained results in light of the consequences of the RNA-Seq theory.
Student will be able to asses the results from both gene and transcript level analysis. Will also be able to draw a conclusion of influence of extension of the expression profiling from gene to the transcript level.
You can find more details like the schedule or information about exams on the course-page in BOKUonline.