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  RNA-seq: From quality control to pathway analysis

  Bern, 23-24 September 2019

  In room Nr. 304, 3 OG Ost, Universität 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.
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  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