I found 10,000 variants. The lab expected 5. Did I mis-call indels? Is there a batch effect? Did someone accidentally use the mouse reference genome again? (It happened once. Once.)
Welcome to bioinformatics. It’s not just running BLAST on a Sunday afternoon.
At 1:00 PM, the wet-lab team sends me an email: “Hi David, we ran the PCR. Can you just ‘quickly’ align this to the genome and find every variant associated with that rare disease? Thanks! Need it by 3 PM.” I smile. I type. I invoke the sacred magic: david bioinfo
Hi! I’m David. Ask me what I do, and you’ll get a different answer depending on the day.
You can have the cleanest pipeline, the most parallelized code, and a server with 1TB of RAM. But if you don’t understand the biological question, you’re just moving bytes around. I found 10,000 variants
Why ‘rm -rf’ is scarier than a pipette tip, and other truths of digital biology. Introduction: Hello, World (of Omics)
So to my fellow Davids: keep one foot in the terminal and one foot in the literature. Validate your outliers. And for the love of all that is holy—. P.S. If you see me staring blankly at a scatter plot at 4 PM, I’m not stuck. I’m just visualizing principal components and questioning my career choices. 😉 Is there a batch effect
Sometimes, I’m a plumber (unclogging data pipelines). Sometimes, a detective (finding a single SNP in 3 billion base pairs). And once a month, I’m a philosopher (arguing whether a p-value of 0.051 is really non-significant).