Section outline

  • Monday 15 February

    9:15 - 10:30: Introduction to RNA-sequencing

    • Experimental design: challenges, considerations, strategies

    10:30 - 11:00: Coffee break

    11:00 - 12:30: Sequencing archives, SRA, ENA and DDBJ

    • File format - Quality Control - subsetting

    12:30 - 13:30: Lunch break

    13:30 - 15:00: Alignment to a reference genome/transcriptome

    • TopHat
    • STAR

    15:00 - 15:30: Coffee break

    15:30 - 17:00: RPKM/FPKM (Reads/Fragments Per Kilobase of transcript per Million mapped reads) Vs. Read counts

    • Practicals "htseq"

    Tuesday 16 February

    9:00 - 10:30: Preparing data for diff expression analysis

    • R- session

    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