More Crab results - DESeq ABC v GHI; more heatmaps

Today I did another DESeq2 analysis comparing crabs A, B, C to crabs G, H, I at Day 2 in order to get any DEGs for temperature on infection. I also tried making some more heatmaps, and I think there may be some cool ones…

DESeq2 Crabs ABC vs GHI at Day

Rmd: scripts/DESeq-ABC-GHI.Rmd

Results: 5 DEGs: analyses/DEG-ABCGHI.tab

4 of the 5 DEGs were able to join with transcriptome v. 1.5 blast output and uniprot_sp_go: annot_DEGlist-ABCGHI.tab

Was join-ed in this Rmd: annoate-ABCGHI-DEGlist.Rmd

Heatmaps!!

In all of the following, I used the DESeq2 to get variance stabilized transformed data. Scroll to the end for plots.

Then, I tried really hard to figure out if it was possible to get variance stabilized transformed lists for all 2020 Genewiz samples, but I couldn’t figure it out.
So I tried using DESeq2 on the individual crab samples to make some more heatmaps using the DEG lists from the above scripts: scripts/heatmaps.html

I also include heatmaps (red) with the normalized counts… and they look like nothing. The range of the normalized counts is WAY too big… so you can’t see anything. That’s why I decided to try the DESeq2 method for the individual crab comparisons heatmaps.

Resources I used to figure those things out:

https://colauttilab.github.io/RNA-Seq_Tutorial.html

https://www.rdocumentation.org/packages/DESeq2/versions/1.12.3/topics/varianceStabilizingTransformation

https://rdrr.io/bioc/DESeq2/man/varianceStabilizingTransformation.html

Next steps before lab meeting tomorrow:

  • Think of some other ways to make heatmaps
  • Try DESeq2 with time as factor
Written on May 25, 2020