RNA-seq Isoform Estimation Tools

[PMID:26944083] [Briefings in Bioinformatics]

Comparative evaluation of isoform-level gene expression estimation algorithms for RNA-seq and exon-array platforms

“Based on RT-qPCR validations, eXpress and Multi-Mapping Bayesian Gene eXpression (MMBGX) programs achieved the best performance for RNA-seq and exon-array platforms, respectively, for deriving the isoform-level fold change values. While eXpress achieved the highest correlation with the RT-qPCR and exon-array (MMBGX) results overall, RSEM was more highly correlated with MMBGX for the subset of transcripts that are highly variable across the samples. eXpress appears to be most successful in discriminating lowly expressed transcripts, but IsoformEx and RSEM correlate more strongly with MMBGX for highly expressed transcripts.” “demonstrate that exon arrays yield comparable results to RNA-seq for evaluating isoform-level expression changes.”


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