Resolution of splicing differences in the sex determination pathway. Detection and visualization of sex-differential splicing in sex determination pathway components by different methods. (A) Analysis of the regulated alternative last exons splicing event in dsx, showing the splicing difference between the female isoform (top, red) and male isoform (bottom, blue). Mosaic plots display female isoform (red) and the male isoform (blue) abundances in each sex for: splice junctions counts, qPCR, counts of reads within exons, and full length isoform abundance estimates (FPKM). (B) Splicing analysis for other components of the sex determination pathway, along with sex-differential splicing results obtained: Sxl, skipped exon; msl-2, retained intron, tra, alternative acceptor, and fru, alternative donor. Significance measures from Spanki (Benjamini-Hochberg adjusted p-value) are shown beneath each mosaic plot. (C) Performance of other RNA-Seq analysis tools in detecting sex determination pathway components. DEXSeq , which relies only on exon-level counts, detected significant differences in fru, Sxl, and dsx, but not in msl-2 or tra. Similarly, a Bayesian analysis with MISO  failed to detect differential splicing of msl-2 transcripts. For Cuffdiff , we examined results for the splicing difference test (Jensen-Shannon Divergence metric), and also for isoform abundance differences.
Sturgill et al. BMC Bioinformatics 2013 14:320 doi:10.1186/1471-2105-14-320