Genomics - Approaches and Algorithms - MB151P130

• Title: Genomics - Approaches and Algorithms
• Czech title: Genomika - postupy a algoritmy
• Guaranteed by: Department of Cell Biology (31-151)
• Faculty: Faculty of Science
• Actual: from 2021 to 2023
• Semester: winter
• E-Credits: 5
• Examination process: winter s.:combined
• Hours per week, examination: winter s.:2/2, C+Ex [HT]
• Capacity: unlimited
• Min. number of students: unlimited
• 4EU+: no
• Virtual mobility / capacity: no
• State of the course: taught
• Language: English
• Note: enabled for web enrollment
• Guarantor: RNDr. Martin Převorovský, Ph.D.; Mgr. Petr Daněček, Ph.D.
• Teacher(s): Mgr. Petr Daněček, Ph.D.; RNDr. Martin Převorovský, Ph.D.
• Class: Původní předmět
• Incompatibility : MB151P111
• Is incompatible with: MB151P111, MB151P129

Annotation

Last update: RNDr. Martin Převorovský, Ph.D. (23.11.2020)

The course introduces methods and technologies of NGS sequencing of DNA, and analyses of genomic data. Key relevant algorithms will also be explained. Experiment design, and both the wet-lab and computational parts of the analysis are covered in detail for selected common methods (RNA-seq, ChIP-seq, genome sequencing, variant calling etc.).
During the practical part, students get hands-on experience with sequencing data and typical analysis workflows. For the practical sessions, students are required to possess basic knowledge of working in linux and on the command line (if needed, you can learn the prerequisites yourself during the semester, as the practical part only takes place during the exam term).
The course is primarily intended for Bioinformatics students. We recommend that Biology students attend the Methods in Genomics (MB151P129) course instead.

The course is taught with the support of the project ESF pro VŠ II na UK, Reg. num.: CZ.02.2.69/0.0/0.0/18_056/0013322

Literature

Last update: RNDr. Martin Převorovský, Ph.D. (10.06.2020)

Course materials from lectures are available via Moodle.

Requirements to the exam

Last update: RNDr. Martin Převorovský, Ph.D. (10.06.2020)

credit (zápočet) - active participation at practical sessions

exam - ability to apply information from lectures and practicals will be determined using a combined written&oral exam (e.g., solving model problems)

Syllabus

Last update: RNDr. Martin Převorovský, Ph.D. (10.06.2020)

Microarrays
Sequencing technologies
QC
Resources - databases & large projects
Mapping
Assembly
Variant calling
CNV calling
Phasing/Imputation
RNA-seq, single-cell analyses
ChIP-seq
Structural variation
Metagenomics
Data integration, visualization

 

The 3-day practical part is focused on analyzing NGS data.

Entry requirements

Last update: RNDr. Martin Převorovský, Ph.D. (10.06.2020)

You must be able to log into CAS (https://ldap1.cuni.cz/) for the practical sessions.

Basic knowledge of working in linux and on the command line is required for the practical sessions.