Welcome to bioinformatics. It’s not just running BLAST on a Sunday afternoon.
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.
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. 😉 david bioinfo
Why ‘rm -rf’ is scarier than a pipette tip, and other truths of digital biology. Introduction: Hello, World (of Omics)
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. Welcome to bioinformatics
The first rule of : Always check your checksums.
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. This is when I practice patience
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.)