Annotation and differential analysis of alternative splicing using de novo assembly of RNAseq data

Genome-wide analyses reveal that more than 90% of multi exonic human genes produce at least two transcripts through alternative splicing (AS). Various bioinformatics methods are available to analyze AS from RNAseq data. Most methods start by mapping the reads to an annotated reference genome, but some start by a de novo assembly of the reads. In this paper, we present a systematic comparison of a mapping-first approach (FO_SCPLOWAC_SCPLOWRLO_SCPLOWINEC_SCPLOW) and an assembly-first approach (KO_SCPLOWISC_SCPLOWSO_SCPLOWPLICEC_SCPLOW). These two approaches are event-based, as they focus on the regions of the transcripts that vary in their exon content. We applied these methods to an RNAseq da