David Bioinfo Site

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.)

Hi! I’m David. Ask me what I do, and you’ll get a different answer depending on the day. david bioinfo

My day doesn’t start with a microscope. It starts with a terminal. Usually, I’m staring at a 50GB FASTQ file that decided to corrupt itself at 2:00 AM. 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) Is there a batch effect

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. 😉

Welcome to bioinformatics. It’s not just running BLAST on a Sunday afternoon.

I’ve learned the hard way that a single misplaced flag in cutadapt can turn your precious RNA-seq reads into biological confetti. My morning ritual? Coffee. htop to see if my server is crying. And grep to make sure my adapter indices didn’t cross-contaminate.