Workflow for parallel gene-level and exon-level analyses. The workflow illustrates two parallel lines of analysis corresponding to gene-level (left) and exon-level (right) signal processing. The analyses converge at the level of MIDAS or the Splicing Index, which implement statistical testing for alternative splicing. Signal estimation and MIDAS occur within the ExACT software and the filtering is accomplished mainly with simple Perl scripts. Yellow boxes represent files or data sets and green boxes represent processes or programs. Solid lines represent the main data flow and dotted lines are auxiliary flows, mainly for filtering.