Fig. 2

Pipeline. a - how we define gene structures starting from different transcripts. We obtain “melted genes” collapsing together the structures of all the transcripts assigned to a gene. aPA: alternative polyadenylation site. cPa: canonical polyadenylation site. Thicker blue rectangles represent coding exons, while the others depict untranslated regions. b - an example of how roar works with the single APA annotation: in sample #1 the shorter isoform is more expressed than the longer one with respect to sample #2. Blue wavy shapes represent aligned mRNAseq reads. c - how transcript fragments are defined in multiple APA analyses to efficiently count reads for all the possible APA choices. aPA1-2-3 are three different APA sites reported for this sample gene