You select the Transcriptome application type and Alternative splicing if you are aligning transcriptome (RNA-Seq) data and the transcriptome project must contain alternative splicing information. When Alternative splicing is selected, NextGENe uses a proprietary four step alignment algorithm to ensure that reads that span exon junctions can be aligned, and then after alignment, transcripts are called. The settings that are available for a transcriptome project with alternative splicing are very different from the alignment settings for all other application types.