Bioinformatics

Your amplicon FASTQ files are back from the sequencer, and the default CRISPResso2 numbers are already lying to you about your HDR and base editing rates. Here is how to run CRISPResso2 properly from raw paired-end reads to publication-ready allele tables.

Your DESeq2 results table has thousands of rows, and sorting it in Excel tells you almost nothing about your experiment. Here is how to build volcano plots and MA plots in R with ggplot2 — and how to read what they are actually telling you.

Short-read amplicon NGS is the gold standard for CRISPR indel detection — but it has a blind spot for structural variants, large deletions, and complex rearrangements. Long-read sequencing from Oxford Nanopore or PacBio fills that gap. Here is when it matters and how to actually run the analysis.

You can run a Western blot but you are terrified of the terminal. Here is everything a bench biologist actually needs to know about the command line — navigating files, counting sequences, searching data, and writing one-liners that replace an hour of Excel work.

You installed samtools and it broke your entire Python setup. Or DESeq2 needs R 4.3 but your system has R 4.1. Here is how Conda solves the dependency nightmare that every biologist runs into — with real commands, real installs, and real output.