Blockveranstaltung: Bioinformatics of high-throughput NGS: single-cell RNA-seq and Oxford Nanopore third-generation sequencing technologies - Details

Blockveranstaltung: Bioinformatics of high-throughput NGS: single-cell RNA-seq and Oxford Nanopore third-generation sequencing technologies - Details

Close message box
You are not logged into Stud.IP.

General information

Course name Blockveranstaltung: Bioinformatics of high-throughput NGS: single-cell RNA-seq and Oxford Nanopore third-generation sequencing technologies
Subtitle
Course number 340671
Semester SoSe 2024
Current number of participants 6
maximum number of participants 6
notwendige Teilnehmeranzahl 3
Home institute Göttinger Graduiertenzentrum für Neurowissenschaften, Biophysik und molekulare Biowissenschaften (GGNB)
participating institutes Georg-August University School of Science (GAUSS) (für Mathematik und Naturwissenschaften)
Courses type Blockveranstaltung in category Teaching
First date Wednesday, 15.05.2024 09:00 - 17:00
Type/Form
Pre-requisites Basic programming skills (R, Python) are not strictly necessary, but would be beneficial.
Miscellanea The course will take place in presence at Seminarraum - Multifunktionsgebäude, EG Room (Deutsches Primatenzentrum GmbH, Kellnerweg 4, 37077 Göttingen).

The course instructors are Laura Ahumada Arranz and Charlotte Höltermann.

Rooms and times

No room preference
Wednesday, 15.05.2024 09:00 - 17:00
Thursday, 16.05.2024 09:00 - 17:00

Fields of study

Comment/Description

This course is designed to provide students with a comprehensive understanding of NGS technologies and their applications, with a focus on data from third-generation sequencing technologies (Oxford Nanopore) and single-cell RNA-seq (scRNA-seq). The course will consist of theoretical lectures in the morning and guided programming exercises in the afternoon to ensure a hands-on learning experience.

On the first day, in the theoretical segment, students will learn about preparing a library and conducting a sequencing run using Oxford Nanopore technology, focusing on enriching samples in regions of interest through techniques like Cas9 targeted enrichment or adaptive sampling and the practical applications of such methods. In the practical component, students will be guided on handling Nanopore NGS data output, understanding different formats, preparing FASTQ data, aligning sequences using tools like minimap2, running Nextflow pipelines for sample enrichment analysis, performing de novo and reference-based assemblies, evaluating assembly quality, annotating the output assembled sequences and visualizing results in IGV.

On the second day of the course, a short theoretical introduction to the analysis of scRNA-seq data will be given where the students will learn the options they have when planning a scRNA-seq experiment, where to find information, tutorials and help and where to find public databases. During the practical session students will learn how to deal with scRNA-seq data, how to avoid common pitfalls when analyzing scRNA cell data and what are the available software packages for data analysis.

A handout will be given to all students with a summary on the topics learned, and a list of websites and publications with more in-depth information. Attendance and participation in the programming exercises will be the requirements for obtaining credits. A laptop with a working internet connection (eduroam) is needed for the exercises.
Important:

Once participation has become binding after the signing-out period, cancellation is only possible via the GGNB or GAUSS Office with a) sick certificate, or b) statement by supervisor for scientific reasons. If you do not provide this, you will be excluded from courses for the next 12 months, as well as travel grants and other financial support. No exceptions.

By signing up you agree (1) to carefully check whether you will be able to attend the course (do not register for 2 courses taking place on the same dates - the above mentioned sanctions apply!), (2) to frequently check your student e-mail account, as all information on courses will exclusively be sent to that account; (3) that your name and e-mail address may be forwarded to the course instructor(s) for communication before and after the course; (4) to complete the course evaluation; (5) inform us if you no longer wish to maintain a waiting list position; (6) that you only receive credits for attending the entire workshop - you will not get partial credits for part-time attendance.

Admission settings

The course is part of admission "GGNB_Methods_2024_SoSe_April_Juni".
You can register and sign out for methods courses in June 2024 from 1-20 April 2024. The slots will be assigned around 25 April 2024.
In exceptional circumstances, you can still sign out until 30 April 2024.
Your participation becomes binding on 2 May 2024. Thereafter, cancellation is only possible via the GGNB Office with a) sick certificate, or b) statement by supervisor (for scientific reasons). If you do not provide this, you will be excluded from courses for the next 12 months, as well as travel grants and other financial support.

By signing up you agree (1) to carefully check whether you will be able to attend the course (do not register for 2 courses taking place on the same dates – the above mentioned sanctions apply!), (2) to frequently check your student e-mail account, as all information on courses will exclusively be sent to that account; (3) that your name and e-mail address may be forwarded to the course instructor(s) for communication before and after the course; (4) to complete the course evaluation.
The following rules apply for the admission:
  • At least one of these conditions must be fulfilled for enrolment:
    • Subject is Computer Science -PCS-
    • Subject is Molekulare Biologie
    • Subject is PhysicsBiologComplexSyste
    • Subject is Systems Neuroscience
    • Subject is Materialforschung Holz
    • Subject is MolecularBiology of Cells
    • Subject is Geographie
    • Subject is Environmental Informatics
    • Subject is Behavior and Cognition
    • Subject is Theoret Computat Neurosci
    • Subject is Neurowissenschaften
    • Subject is IRTG 2172 - PRoTECT
    • Subject is Psychologie
    • Subject is Molekulare Medizin
    • Subject is Umweltinformatik
    • Subject is Emerging Infect. Diseases
    • Subject is Genome Science
    • Subject is Environmental Informatics
    • Subject is Geoscience
    • Subject is Biologie
    • Subject is Genes in Development, Disease and Evolution
    • Subject is Biologische Diversität und Ökologie
    • Subject is Physik
    • Subject is Microbiology-Biochemistry
    • Subject is Mathematical Sciences
    • Subject is Geography
    • Subject is Chemie
    • Subject is BioNutz-MolwissBiotechnol
    • Subject is Biomol:Struc-Func-Dynamic
    • Subject is Cardiovascular Science
    • Subject is Catalysis Sust.Synt.CaSuS
    • Subject is SensoryMotor Neuroscience
    • Subject is MolecularPhysi oftheBrain
    • Subject is MetalSites i.Biomolecules
  • At least one of these conditions must be fulfilled for enrolment:
    • Degree is PromProgramm Cotutelle
    • Degree is PromStudiengang Cotutelle
    • Degree is Promotionsprogramm
    • Degree is Promotionsstudiengang
    • Degree is Promotion m.Abschlussprfg
    • Degree is Promotion Cotutelle
  • The enrolment is possible from 01.04.2024, 00:00 to 20.04.2024, 23:59.
  • A defined number of seats will be assigned to these courses.
    The seats in the affected courses have been assigned at 25.04.2024 on 23:59. Additional seats may be available via a wait list.
  • Enrolment is allowed for up to 2 courses of the admission set.
Assignment of courses:

Registration mode

The enrolment is binding, participants cannot unsubscribe themselves.