2025/03/13 by Sylvain Mareschal, Valentin Wucher, Sarah Huet +7 · 1 voice
Biochemistry, Genetics and Molecular Biology · #RNA Research and Splicing #RNA and protein synthesis mechanisms #Molecular Biology Techniques and Applications
paper · pdf · doi:10.1101/2025.03.10.642333
openalex publication_date 2025/03/13 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/22
Abstract Summary Despite RNA-sequencing solutions have existed for 15 years, successfully replacing micro-arrays for gene expression profiling, their potential to analyse splicing is still to be achieved in clinical settings. Powerful tools were developed to quantify known iso-forms, to compare sample groups or to identify outliers in large datasets, but most fail to address the most common situation in routine diagnostics: identifying non-recurring events in low-dimension data. To fill this gap, we developed SAMI (Splicing Analysis with Molecular Indexes), an UMI-aware pipeline focusing on splicing events which differ from provided annotation. The ability of SAMI and concurrent software to detect intragenic splicing aberrations and gene fusions was assessed, both on real data from a commercial control sample and simulated data generated with ASimulatoR. Availability and Implementation Nextflow pipeline and Singularity container recipe freely available under GPL 3 licence at https://github.com/HCL-HUBL/SAMI Contact [email protected]