Topic outline

  • General

    De Novo Transcriptome Assembly - Trinity

    Bern, 10-11 October 2016

    University of Bern, Hochschulstrasse 4, room 331 3.OG/West

    This page is addressed to registered participants. To access event description, exact location and application form, please click here.

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  • Programme

    The course will run every day from 9h to 12h30 and then from 13h30 to 17h, and will include two coffee breaks per day.

    Day 1:

    Morning:  Intro to RNA-Seq and transcriptome analysis

    • lecture on intro to rna-seq and the Trinity algorithm for transcript reconstruction
    • practical:¬†evaluation of NGS read quality
    • practical: in silico normalization of reads
    • practical: trinity assembly

    Afternoon: Expression Quantitation and Assembly Quality Assessment

    • lecture on expression quantitation
    • practical: using RSEM and kallisto for expression quantitation
    • practical: evaluating transcript assembly quality

    Day 2:

    Morning: Differential expression analysis

    • lecture on differential expression analysis and the importance of statistics
    • practical: using edgeR to identify DE transcripts and genes
    • practical: transcript clustering

    Afternoon: Transcript functional annotation and DE cluster functional enrichment studies

    • lecture on transcript functional annotation
    • practical: using Trinotate to functionally annotate transcripts and genes
    • practical: using goseq to identify functional enrichments of DE clusters