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Abstract:
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The analysis of RNA-seq data has been focused on three main categories, including gene expression, (relative) exon usage and transcript expression. Many approaches have been proposed independently for each category using a negative binomial model. We proposed a family of negative binomial models (FNB), which integrates the gene, exon and transcript analysis under one unified negative binomial model. The beauty of the model is that it easily incorporates the uncertainty of assigning reads to transcripts and greatly simplifies the estimation for relative usage. We use fully tractable closed-forms ("conjugacy") for the posterior inference. Our results showed that the FNB model provides competitive alternatives to existing tools in the RNA-seq analysis.
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