ChIP-seq data analysis, 1 hp (Location: Stockholm)

Beskrivning

National course open for PhD students, postdocs, researchers and other employees in need of ChIP-seq data analyses skills within all Swedish universities.
This course provides a practical introduction to analyzing ChIP-seq data. It is aimed for those already working with NGS data analyses but in need of learning best practice bioinformatics methods for processing and analyses of ChIP-seq data.

Inlärningsmål

Upon completion of the course, attentive participants will be able to plan and run most common ChIP-seq data analyses.

Innehåll

This course will introduce the best practice bioinformatics methods for processing and analyses of ChIP-seq data including:

Quality controls of raw sequencing reads
Reads trimming and filtering
Alignment to the reference genome
Peak-independent quality metrics
Peak calling
Peak-dependent quality metrics and visualization
Differential binding analysis
Functional analysis, incl. finding nearest genes, exons and custom features, obtaining enriched Gene Ontology terms and pathways

Undervisning

Applications are only accepted via the course webpage:

https://www.scilifelab.se/events/chip-seq-data-analysis/

Course fee: 1300 SEK.

Entry requirements
Required for being able to follow the course and to complete computer exercises:

- At least basic knowledge in Linux
- Ability to bring your own laptop with R installed for the computer exercises
Programming / scripting experience, preferably in R

Desired:
- Experience working on Uppmax or another HPC
- Previous experience with NGS data analyses
- Completing SciLifeLab / NBIS courses “Introduction to Bioinformatics using NGS data” and “R Programming Foundations for Life Scientists”

Examination

Participation on all lectures, exercises and discussion.

Litteratur

The literature will be provided during the course.

Lärare

Olga Dethlefsen, Agata Smialowsk

Kontakt

olga.dethlefsen@nbis.se

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