anishl135/twintrondetect

Twintron Detector is a command-line RNA-seq analysis tool that finds candidate splice junctions nested inside annotated U12 introns, compares their usage between two conditions, and emits tables, reports, and genome-browser tracks. The main workflow validates inputs, discovers nested junctions using junction BED and BAM evidence, then classifies candidates, annotates known-junction status, scores evidence, calculates differential usage, and writes results. README capabilities guide the map; sampled excerpts confirm key detection, classification, annotation, validation, scoring, and reporting details, but not every orchestration call.