A Deep Dive Into SQANTI3 to Master Isoform Quality Control
Tianyuan Liu, Doctoral Candidate at the Genomics of Gene Expression Lab (I2SysBio-CSIC), explains how to work with long-read transcriptomics data and have created a video-tutorial of the tool SQANTI3.Â
Whether you are using PacBio or Oxford Nanopore technologies, accurate transcriptome characterization is the cornerstone of downstream analysis. We are excited to highlight a comprehensive video tutorial that demystifies SQANTI3, the go-to tool for quality control and filtering of long-read transcriptomes.
This new tutorial provides a step-by-step guide through the SQANTI3 pipeline, a crucial component of the Functional Iso-Transcriptomics workflow. It is designed to help researchers move beyond raw sequencing data to curated, high-confidence transcript models.What You Will LearnThe tutorial breaks down the software’s three main modules:
- SQANTI3 QC: Learn how to prepare your input files (transcriptome, reference genome, annotation) and understand the structural classification of your isoforms (e.g., Full Splice Match vs. Novel).
- SQANTI3 Filter: Discover how to remove artifacts and false positives using both rule-based filtering and automated machine learning classifiers (Random Forest).
- SQANTI3 Rescue: Explore the new “Rescue” module, which allows you to recover valid reference transcripts that might have been unintentionally discarded during the filtering process.
Why This MattersLong-read sequencing offers unprecedented insight into full-length isoforms, but it also comes with unique challenges regarding artifacts and biological noise. SQANTI3 provides the rigorous QC framework necessary to ensure your biological conclusions are based on real, high-quality data.
Watch the full tutorial here:https://www.youtube.com/watch?v=TTjDAwuhB68
Watch the full tutorial here:https://www.youtube.com/watch?v=TTjDAwuhB68Â
Read the full SQANTI3 paper here: https://doi.org/10.1038/s41592-024-02229-2Â Â
