Topic outline

  • RNA-seq: From quality control to pathway analysis

    Bern, 23-24 September 2019

    In room Nr. 304, 3 OG Ost, Universit├Ąt Bern, Hochschulstrasse 4.

    This page is addressed to registered participants. To access the course description and the application form, please click here.

    For any assistance, please contact training@sib.swiss.

    • Schedule

      Schedule

      Day1:
      9:15 - 10:30:  - Introduction to RNA-sequencing
                             - Experimental design: challenges, considerations, strategies
                             - Examples
      10:30 - 11:00: Coffee Break
      11:00 - 12:30: - Sequencing archives, SRA, ENA and DDBJ
                              - Practicals using SRA-tools
                              - File format - Quality Control - subsetting
      12:30 - 13:30: Lunch break
      13:30 - 15:00: - Interpretation of a Fastqc report and acting upon for cutting/trimming reads
                              - Trimming/filtering quality control - Practicals
      15:00 - 15:30: Coffee break
      16:00 - 17:00: - Alignment to a reference genome/transcriptome
                              - HISAT2 
                              - STAR

      Day2:
      9:00 - 10:30: Expression quantification:
                             - FPKM (Fragments Per Kilobase Of Exon Per Million fragments mapped) vs. Counting mapped fragments
                             - Practicals using htseq-count
      10:30 - 11:00: Coffee Break
      11:00: 12:30: Differential expression
                            -Practicals using DESeq2 (R-statistics)
      12:30 - 13:30: Lunch Break
      13:30 - 15:00: Gene Ontology and GO enrichment analysis
                                - practicals using Goseq (R-statistics)
      15:00 - 15:30: Coffee break
      15:30 - 17:00: Differentially enriched Pathways finding
                                 - practicals using Pathview (R-statistics)

      17:00- 17:30: Optional exam