20 posts
A working guide to diagnosing and handling batch effects in bulk RNA-seq, from design and TMM normalization through limma, ComBat-seq, and RUV, with the checks that tell you whether the correction helped.
Why the data structure chosen for a genome, a variant set, an expression matrix, or a phylogeny decides which questions can be asked and what runs in reasonable time, prompted by a Boundary talk on coding agents.
Genetic Genie's methylation panel reads about two dozen genotypes out of a consumer array file. This guide shows how to extract and verify those calls yourself, what they can and cannot tell you, and how to measure actual DNA methylation if that is what you were after.
How to run a genome-wide association study in R end to end, from VCF to QC to association testing to polygenic scores, and what you can and cannot do with a single genome.
A practical pipeline for turning a tellmeGen raw data export into a build-verified VCF, running quality control, annotating it, and understanding what a genotyping array can and cannot tell you.
A practical comparison of Oxford Nanopore, Illumina, Element, PacBio, and Sanger for sequencing one person's genome: why we would choose nanopore long reads, what to ask a provider for, and the pipeline we would run on the output.
A practical comparison of DNA methylation tests: which array, which clocks, how to get the raw IDATs, and how to process them yourself with sesame and dnaMethyAge. Plus the noise sources that make a single epigenetic age number close to meaningless.
A step-by-step method for pulling rs1801133 and rs1801131 out of a 23andMe, AncestryDNA, or WGS file yourself, getting the strand right, and understanding what the result does and does not tell you.
A working guide to interpreting raw genotype files from 23andMe or Ancestry, converting them to VCF, annotating variants, and knowing where array data stops being useful.
A technical account of whole genome sequencing as a data product: coverage and chemistry, file formats, a pipeline we would run, and the questions a genome can and cannot answer.
Master the mrna sequence to dna sequence conversion. Covers basic rules, strand orientation, reverse complements, and design considerations for researchers in
Master the codon bias table to improve protein expression. Learn to calculate RSCU and CAI metrics while avoiding common bioengineering pitfalls in 2026.
Master library preparation for next generation sequencing with our guide. Covers DNA/RNA workflows, QC, troubleshooting, and prep's computational impact.
Master RNA sequencing library preparation with our guide. Learn workflows, QC steps, and how prep choices impact analysis for optimal results.
Master protein domains and motifs. Discover their function, detection tools, and application in cell design and DNA engineering workflows.
Get the complete guide to the respiratory viral panel. Learn detection tech, assay design, validation, bioinformatics, & R&D tools.
Get a comprehensive whole exome sequencing review for R&D teams. Explore WES methodology, bioinformatics, limitations, & data integration with models.
The definitive guide to the adaptor sequence illumina system. Find sequences, learn trimming with Cutadapt, and troubleshoot issues for clean NGS data.
Discover how genomic DNA libraries work. This guide covers construction, QC, analysis, and applications in genome sequencing and synthetic biology.
Curious what is whole exome sequencing? Explore how WES works, its role in research, and how to interpret the data in our clear, practical guide for 2026.