TitlePolee: RNA-Seq analysis using approximate likelihood.
Publication TypeJournal Article
Year of Publication2021
AuthorsJones DC, Ruzzo WL
JournalNAR Genom Bioinform
Volume3
Issue2
Paginationlqab046
Date or Month Published2021 Jun
ISSN2631-9268
Abstract

The analysis of mRNA transcript abundance with RNA-Seq is a central tool in molecular biology research, but often analyses fail to account for the uncertainty in these estimates, which can be significant, especially when trying to disentangle isoforms or duplicated genes. Preserving uncertainty necessitates a full probabilistic model of the all the sequencing reads, which quickly becomes intractable, as experiments can consist of billions of reads. To overcome these limitations, we propose a new method of approximating the likelihood function of a sparse mixture model, using a technique we call the Pólya tree transformation. We demonstrate that substituting this approximation for the real thing achieves most of the benefits with a fraction of the computational costs, leading to more accurate detection of differential transcript expression and transcript coexpression.

DOI10.1093/nargab/lqab046
Downloadshttps://www.ncbi.nlm.nih.gov/pubmed/34056596?dopt=Abstract
Alternate JournalNAR Genom Bioinform
Citation Key16149
PubMed ID34056596
PubMed Central IDPMC8152449