Title | Polee: RNA-Seq analysis using approximate likelihood. |
Publication Type | Journal Article |
Year of Publication | 2021 |
Authors | Jones DC, Ruzzo WL |
Journal | NAR Genom Bioinform |
Volume | 3 |
Issue | 2 |
Pagination | lqab046 |
Date or Month Published | 2021 Jun |
ISSN | 2631-9268 |
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 PĆ³lya 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. |
DOI | 10.1093/nargab/lqab046 |
Downloads | https://www.ncbi.nlm.nih.gov/pubmed/34056596?dopt=Abstract |
Alternate Journal | NAR Genom Bioinform |
Citation Key | 16149 |
PubMed ID | 34056596 |
PubMed Central ID | PMC8152449 |