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