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
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
join-ed in this Rmd: annoate-ABCGHI-DEGlist.Rmd
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:
Next steps before lab meeting tomorrow:
- Think of some other ways to make heatmaps
DESeq2with time as factor