Omics Applications - evaluation doubts

30 dezembro 2019, 15:25 • Susana Vinga

Following some questions regarding the omics module, namely the material for the test/exam, see Prof. Nuno Morais reply:

The evaluation of topics covered in the last three weeks of classes aims to assess the students’ level of understanding of the concepts underlying the work done for LAB#6. It will essentially focus on the interpretation of results (metrics and plots) from the several stages of RNA-seq data analysis. I will mainly evaluate your abilities to:

  • interpret metrics and graphics associated with sequencing quality control;
  • interpret the outputs of RNA-seq aligners, understand the distinction between genomic and transcriptomic alignments, associate the quantification of transcript expression with that of gene expression;
  • understand the concepts of RNA-seq library size (read coverage) and complexity, interpreting plots summarising their distributions, and their importance in data normalisation;
  • associate the main axes of data variance to phenotypical and technical variables, identifying batch effects;
  • translate an experimental design and a set of questions on differential gene expression through a design matrix for subsequent linear model fitting;
  • interpret the different statistics of differential expression and understand the criteria for their usage in gene set (e.g. pathways) enrichment analyses;
  • interpret gene set enrichment analysis results (statistics and plots).