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PFS0161

RNA-seq data analysis

The course contains three intense days of lectures and computer exercises. It is initiated with an introduction to Linux and working on UPPMAX. In the following, lectures from experts in RNA-seq and biostatistics will cover a range of cutting-edge issues in RNA quality control, transcript assembly, differential expression analysis and downstream analysis. An extensive set of computer exercises will familiarize you with concepts and programs for mapping, quality control of your RNA-seq data, and differential expression analysis.

Topics that will be covered include:

- Introduction to Linux and UPPMAX

- Introduction RNA seq

- RNA seq read mapping programs

- Quality assessment of RNA-seq data

- Differential expression analysis.

Kursplan

PFS0161 RNA-seq data analysis, 2,0 Hp

Ämnen

Biologi

Utbildningens nivå

Forskarnivå

Förkunskapskrav

The course is primarily for PhD students within the SLU Research School Organism Biology but will be open for all interested PhD students/researchers.

Mål

After the course students are expected to be familiar with the theory and practice of RNA-seq analysis.

Innehåll

The course contains three intense days of lectures and computer exercises. It is initiated with an introduction to Linux and working on UPPMAX. In the following, lectures from experts in RNA-seq and biostatistics will cover a range of cutting-edge issues in RNA quality control, transcript assembly, differential expression analysis and downstream analysis. An extensive set of computer exercises will familiarize you with concepts and programs for mapping, quality control of your RNA-seq data, and differential expression analysis.

Topics that will be covered include:

- Introduction to Linux and UPPMAX

- Introduction RNA seq

- RNA seq read mapping programs

- Quality assessment of RNA-seq data

- Differential expression analysis.

Examinationsformer och fordringar för godkänd kurs

Attendance at all scheduled activities and approved computer exercises.

Ytterligare information

Teaching on this course is provided by Johan Reimegård and colleagues at NBIS (nbis.se), SciLifeLab (www.scilifelab.se) and UPPMAX (www.uppmax.uu.se). The course is organized by the SLU research school Organism Biology. There is no tuition fee. Participants are expected to bring their own laptop for the practical computer exercises and to arrange and familiarize themselves with software and UPPMAX user accounts according to instructions from the organizer prior to the course start.