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.

Sturgill et al.

Sturgill et al. BMC Bioinformatics 2013 14:320   doi:10.1186/1471-2105-14-320

Open Data