McSplicer: a probabilistic model for estimating splice site usage from RNA-seq data

Abstract

Alternative splicing removes intronic sequences from transcripts in alternative ways to produce different forms (isoforms) of mature mRNA. The composition of expressed transcripts and their alternative forms give specific functionalities to cells in a particular condition or developmental stage. In addition, a large fraction of human disease mutations affect splicing and lead to aberrant mRNA and protein products. Current methods that interrogate the transcriptome based on RNA-seq either suffer from short read length when trying to infer full-length transcripts, or are restricted to predefined units of alternative splicing that they quantify from local read evidence. Instead of attempting to quantify individual outcomes of the splicing process such as local splicing events or full-length transcripts, we propose to quantify alternative splicing using a simplified probabilistic model of the underlying splicing process. Our model is based on the usage of individual splice sites and can generate arbitrarily complex types of splicing patterns. In our method, McSplicer, we estimate the parameters of our model using all read data at once and we demonstrate in our experiments that this yields more accurate estimates compared to competing methods. Our model is able to describe multiple effects of splicing mutations using few, easy to interpret parameters, as we illustrate in an experiment on RNA-seq data from autism spectrum disorder patients. McSplicer is implemented in Python and available as open-source at https://github.com/canzarlab/McSplicer.

NanoSplicer: Accurate identification of splice junctions using Oxford Nanopore sequencing

“…Short-read sequencing technologies (e.g., Illumina sequencing) have been successfully used to identify and quantify local splicing events, such as exon skipping. However, their read lengths (~ 150 nt) are much shorter than typical transcript lengths, making it difficult to combine each splicing event and identify the fulllength isoform(s) present (LeGault and Dewey, 2013; Steijger et al ., 2013; Tang et al ., 2020; Alqassem et al ., 2021; Parker et al ., 2021). As such our understanding of the isoform repertoire expressed in different organisms and those that control cell functions remains incomplete.…”