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…
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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...
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New DEG list comparing temperature - annotation, enrichment; annotation of oyster differentially abundant protein list
Today I worked with the new DEG list from DESeq2 - comparing elevated (10˚C) and decreased (4˚C) temperature treatments. Annotated with uniprot-SP-GO and used DAVID to get enriched biological processes. Additionally, since it could be interesting to compare between oyster and crab projects, I annotated the list of differentially abundant...
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Submitted Thesis Chapters to Committee; Start working with New transcriptome
Today I submitted my two thesis chapters to my committee, and between now and June 2nd (my defense date), I’ll be doing more differential expression analyses with the new transcriptome (not filtered based on taxonomy). Plan for the work and what I’ve done so far detailed in post.
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Create annotated crab transcriptome BLAST `join` with uniprot SP GO
Worked a lot on the crab paper intro and bits of results and discussion here and there. I also made an annotated BLAST output from the crab transcriptome with the uniprot-SP-GO.sorted file.
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