Fig. 9

Visual output for APLP2 from Manananggal. a shows the standard coverage plot for both sample groups. The light shaded regions around each line represent the upper and lower quartile of the coverage. b shows the coverage ratio representation of the coverage plot. Using ratios flattens the coverage for all exons and makes it easier to spot the alternatively spliced exons that appear at ‘bumps’ in the coverage ratio that otherwise remains very constant across all exons. c shows the isoforms that are likely involved in the ASEs. The antisense transcript track is empty and the sense transcript track only shows one exon of APLP2 that overlaps an intronic region of another transcript on the same strand (indicated by the light blue box). Therefore, it is unlikely that overlapping transcripts influence the coverage of APLP2, especially at the ASEs. Further, the automatic ASE detection algorithm of Manananggal identified both ASEs and indicates them by coloring the respective meta exons in red. The percent numbers at the end of each transcript correspond to MMSEQ isoform expression estimates that can be generated if Manananggal has access to MMSEQ. However, this also shows that MMSEQ assigned a large fraction of the coverage to other transcripts that are probably less important or not expressed at all