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. david bioinfo
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). I found 10,000 variants
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: Is there a batch effect