Just to add to Paul’s answer, MAJIQ will not assign a junction to a gene unless its start and end are within the gene’s starting/ending coordinates. So, in this sense, the longest possible junction that can be seen in quantifications/VOILA is determined by the longest (in genomic coordinates) gene.
Joseph Aicher (he/him/his)
MD/PhD Candidate, GS6
Perelman School of Medicine
Genomics and Computational Biology Graduate Group
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