Transcriptome enrichment

Lots of time in computer lab today and it’s getting slightly less stressful every time. We went back to SQLShare this morning to join our full annotated star transcriptome with our SwissProt protein BLAST. Afterward we ran a statistical program in R  to decide which transcripts are significantly differentiated (p<0.05) between the sick and healthy sea stars. This  DeSeq output file we then joined with our SwissProt database in SQLShare to save spIDs for each annotation and ran through DAVID (some of us more successfully than others) to essentially normalize our differentially expressed transcripts to the entire transcriptome and look at which processes are affected by this infection.

Here’s a recap of most of my scripts today, I hope you enjoy my frenzied note-taking and repeated command attempts!

red is significant, p< 0.05

red is significant, p< 0.05

If learning to script is like learning a language I’d say I might be able to stutter my way through a sentence.

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