De Novo Transcriptome Assembly - Trinity
Bern, 10-11 October 2016
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The course will run every day from 9h to 12h30 and then from 13h30 to 17h, and will include two coffee breaks per day.
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
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