Design of RNA splicing analysis null models for post hoc filtering of Drosophila head RNA-Seq data with the splicing analysis kit (Spanki)

Table 1 Comparison of features among RNA-Seq analysis tools

Feature	Spanki	Tophat	Cufflinks	MISO	DEXSeq	RUM	Flux capacitor	Maq
Simulation tools	x					x	x	x
Empirical error modeling	x						x	x
Custom simulated transcript coverages	x
Junction alignment curation	x	x¹
Gene assignment for junctions	x		x²
Qualitative junction analysis	x
Junction-level comparisons	x
Event-level comparisons	x		x³	x	x⁴
PSI metric reporting	x			x

¹Tophat offers criteria for filtering what is reported after the alignment stage. Spanki provides additional criteria that can be applied after reporting.
²Cufflinks assembles transcripts and merges with annotated genes.
³Cuffdiff reports differential splicing by TSS group, without specifiying the differential splicing event.
⁴DEXSeq provides results for exon-level abundance differences.

ISSN: 1471-2105