Fig. 2.

McSplicer workflow summary. The main steps of the McSplicer analysis are: (A) Map RNA-seq reads to the reference genome sequence. (B) Identify annotated as well as novel splice sites through the reference-based assembly of transcripts using, e.g. StringTie (Pertea et al., 2015). (C) Divide the gene into non-overlapping segments bounded by splice sites, TSS and TES and count the number of reads mapping to distinct combinations of segments. In this example, only the start of the first exon and the end of the last exon are bounded by TSS and TES, respectively, the remaining exon start and end sites correspond to splice sites. (D) Estimate splice site usages using McSplicer. (E) Leverage splice site usages in various kinds of downstream analyses, such as the quantification of different types of alternative splicing events