Yesterday, I described how I planned to start with a comparison of Day 0 and Day 17 libraries at ambient temperatures. I was able to complete that! Methods followed the same protocol outlined previously - use Kallisto to create pseudoalignments for libraries, use a script from Trinity pipeline to create matrix of counts, put matrix of counts into DESeq2 and analyze. Here are links to the following results:

  • My DESeq2 script

  • Results, which contain the following:
  • Table of genes with significantly different expressions (adjusted pval <= 0.005), both with and without column headers
  • A variety of MA plots with the following conditions:
    • All results
    • All results, LFC estimates shrunk using apeglm
    • Results with a p-value <= 0.05
    • All results, with p-values <= 0.005 highlighted
  • Dispersion estimates

The most important of those is likely the table of genes with significantly different expressions, but before I do much with that, I’m going to do the next 3 comparisons, as follow:

  • Day 0+2 Elevated vs Low (127/173/72/272/280/294 vs 151/254)
  • Day 0+2 Elevated vs Ambient (127/173/72/272/280/294 vs 118/132/178/334/349/359)
  • Day 0+2 Ambient vs Low (118/132/178/334/349/359 vs 151/254)

Hopefully I’ve got enough storage space for all those libraries!