RNA splicing is integral to eukaryotes and contributes significantly to protein regulation and diversity, occurring in >90% of human genes. There are multiple alternative splicing modes: exon skipping (most common splicing mode in humans and higher eukaryotes), mutually exclusive exons, alternative donor or acceptor sites, intron retention (most common splicing mode in plants, fungi, and protozoa), alternative transcription start site (promoter), and alternative polyadenylation. One goal of RNA-Seq is to identify alternative splicing events and test if they differ between conditions. Long-read sequencing captures the full transcript and thus minimizes many of issues in estimating isoform abundance, like ambiguous read mapping. For short-read RNA-Seq, there are multiple methods to detect alternative splicing that can be classified into three main groups:
* Count-based (also event-based, differential splicing): estimate exon retention. Examples are DEXSeq, MATS, and SeqGSEA.
* Isoform-based (also multi-read modules, differential isoform expression): estimate isoform abundance first, and then relative abundance between conditions. Examples are Cufflinks 2 and DiffSplice.
* Intron excision based: calculate alternative splicing using split reads. Examples are MAJIQ and Leafcutter.
Differential gene expression tools can also be used for differential isoform expression if isoforms are quantified ahead of time with other tools like RSEM.