JuncForge

Overview

JuncForge is a computational pipeline for designing qPCR primer pairs that span cryptic exon (CE) splice junctions. It targets applications in RNA splicing research, including studies of TDP-43 loss of function and cryptic exon inclusion in neurodegeneration.

What it does

Given GenBank files annotating a cryptic exon within an intron, the pipeline:

1. Locates CE features and their left/right junctions
2. Designs primer pairs via Primer3 with junction-spanning constraints
3. Filters candidates with pair-wise BLAST against genome and curated RefSeq mRNA
4. Retains only primers expected to amplify the CE-containing transcript

Tech stack

Python, Primer3, BLAST

Links

• GitHub: https://github.com/caotianyu0427/JuncForge