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:
The first rule of : Always check your checksums. david bioinfo
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. 😉 At 1:00 PM, the wet-lab team sends me
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. Need it by 3 PM
bwa mem genome.fa sample_R1.fastq sample_R2.fastq > aligned.sam samtools sort -@8 aligned.sam -o sorted.bam freebayes -f genome.fa sorted.bam > variants.vcf Then I wait. This is when I practice patience. And refresh my email 47 times.
Welcome to bioinformatics. It’s not just running BLAST on a Sunday afternoon.
As David the bioinformatician, my real value isn’t typing fast. It’s knowing when a result is biologically plausible vs. computationally correct but nonsense .
