The AlternativeOutput directory contains results from an alternative exon analysis. These files are typically the most informative results from an AltAnalyze analysis. These include:

• (exon-inclusion-results) Alternative exon scores, annotations and protein/motif predictions for significant probesets
• (exon-inclusion-GENE-results) Summarized exon scores, annotations and protein/motif predictions reported for each unique gene only
• (ft-domain-zscores) Over-representation results for each impacted protein domain/motif
• (microRNA-zscores) Over-representation results for each impacted protein microRNA binding site
• (comparison-evidence) Combines junction and exon-level analyses to highlight unique exons regulated by different analyses and where independent confirmation of alternative exon expression exists.
• (summary-results) Overview summary statistics for each analysis
• (all-genes-comparisons-events) Combined exon results for multiple analyses in a single file
• (all-genes-GENE-comparisons-events) Combined gene results for multiple analyses in a single file