Heatmap Practice

Today I’ve been playing with heatmaps and have been able to make quite a few. Now, I’m just going to keep making a bunch from the individual crab RNAseq data to see if there are any interesting patterns. However, I am struggling to get the Trinity ID counts from the 2020 Genewiz samples (individual crabs) annotated with transcriptome v. 1.5 blast output and Uniprot-SP-GO annotation… which means that I’m kind of just mapping random genes…

Trying to annotate 2020 Genewiz count matrix

Individual crab sample counts: sam/20200430_cbai_deg_multiple_conditions/data/salmon.gene.counts.matrix

Rmd to try to annotate list: scripts/annotate-indiv_crab-genecounts.Rmd

Tried to do the same thing as what I did when annotated the list of DEGs:

  1. join the transcriptome v. 1.5 blast output with uniprot-SP-GO.sorted
  2. join the above created table with the Trinity IDs of the count matrix.

Problem –> NONE of the individual crab samples Trinity IDs match with that of the blast transcriptome and uniprot-SP-GO… which doesn’t make sense.

I’m pretty sure that the 2020 Genewiz count matrix is from the transcriptome v. 1.5…?
Sam’s noteboook post where he makes the count matrix

The reason why I want to annotate this is so that I can map interesting genes in heatmaps, even if they aren’t differentiallyexpressed. For example, I have lsits of stress response genes, so I could pick out some that I know match with certain stress response or immune response functions and plot them over time within crabs and compare between crabs…

Heat map practice


HTML preview of above linked Rmd: here

Pretty easy to make heatmaps!!!

I also made some of the DEG lists for temperature comparison and infection status comparisons.

Used this Rmd here to get a list of the 423 temperature comparison DEGs with gene counts.

Plan for before Thursday meeting with SR at 3pm:

  1. add some general notes about the list of enriched DEGs from the temperature comparison (DAVID output: here)
  2. Watch the tutorial on making heatmaps to see if there’s anything else that would be useful to try: video
  3. Make a TON of heatmaps of individual crab data
    • Compare crabs across time; can plot specific genes of interest (need to get GO info for the Trinity IDs FIRST!)
Written on May 19, 2020