Assume that HTSeq counts were obtained for the chr22 genes in for two conditions using triplicates.

  1. Compare the raw distributions of the counts
  2. Using DESeq2, determine a list of differentially expressed genes
  3. Analyse the results using DAVID

Credits

This practical is based on Griffith et al. 2015 “Informatics for RNA-seq: A web resource for analysis on the cloud” PLoS Comp Biol 11(8):e1004393 and the online wiki and was developed with the help of Sigrid Le Clerc.

Resources

  • The DESeq2 vignette “Analyzing RNA-seq data with DESeq2”
  • DESeq2: Love et al. 2014 “Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2” Genome Biol 15:550. 10.1186/s13059-014-0550-8.