https://caotianyu0427.github.io/project/ProjectsHugoBlox Kit (https://hugoblox.com)en-usSun, 01 Jun 2025 00:00:00 +0000https://caotianyu0427.github.io/media/icon_hu_702a800cd775dbac.pnghttps://caotianyu0427.github.io/project/https://caotianyu0427.github.io/project/juncforge/Sun, 01 Jun 2025 00:00:00 +0000https://caotianyu0427.github.io/project/juncforge/<h2 id="overview">Overview</h2> <p>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.</p> <h2 id="what-it-does">What it does</h2> <p>Given GenBank files annotating a cryptic exon within an intron, the pipeline:</p> <ol> <li>Locates CE features and their left/right junctions</li> <li>Designs primer pairs via Primer3 with junction-spanning constraints</li> <li>Filters candidates with pair-wise BLAST against genome and curated RefSeq mRNA</li> <li>Retains only primers expected to amplify the CE-containing transcript</li> </ol> <h2 id="tech-stack">Tech stack</h2> <p>Python, Primer3, BLAST</p> <h2 id="links">Links</h2> <ul> <li>GitHub: </li> </ul>