Figure 1.

MAJIQ-L overview. (A) Input. Matched short- and long-read RNA sequencing data with genome annotation. Short reads are mapped with an aligner and then passed to MAJIQ, producing a splicegraph with a matching set of LSVs per gene. Long reads are processed with a long-read algorithm (e.g., IsoQuant) to produce isoform counts. (B) The outputs from the two RNA sequencing sources along with the annotation are compared. Each splice junction or intron retention (IR) is assigned to each of the possible six categories depending on which subset of the three sources supports it. Various statistics regarding the location, coverage, and overlap of those elements are computed to compare the three sources and explore the source of discrepancy (see main text). (C) MAJIQ-L includes a unified visualization package, VOILA v3, for downstream splicing analysis. It allows users to see which splice junction maps to which isoforms and where the different sources of information agree or disagree in detection and quantification.