September 22, 2019  |  

SparseIso: a novel Bayesian approach to identify alternatively spliced isoforms from RNA-seq data.

Authors: Shi, Xu and Wang, Xiao and Wang, Tian-Li and Hilakivi-Clarke, Leena and Clarke, Robert and Xuan, Jianhua

Recent advances in high-throughput RNA sequencing (RNA-seq) technologies have made it possible to reconstruct the full transcriptome of various types of cells. It is important to accurately assemble transcripts or identify isoforms for an improved understanding of molecular mechanisms in biological systems.We have developed a novel Bayesian method, SparseIso, to reliably identify spliced isoforms from RNA-seq data. A spike-and-slab prior is incorporated into the Bayesian model to enforce the sparsity for isoform identification, effectively alleviating the problem of overfitting. A Gibbs sampling procedure is further developed to simultaneously identify and quantify transcripts from RNA-seq data. With the sampling approach, SparseIso estimates the joint distribution of all candidate transcripts, resulting in a significantly improved performance in detecting lowly expressed transcripts and multiple expressed isoforms of genes. Both simulation study and real data analysis have demonstrated that the proposed SparseIso method significantly outperforms existing methods for improved transcript assembly and isoform identification.The SparseIso package is available at[email protected] data are available at Bioinformatics online.© The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: [email protected]

Journal: Bioinformatics
DOI: 10.1093/bioinformatics/btx557
Year: 2018

Read publication

Talk with an expert

If you have a question, need to check the status of an order, or are interested in purchasing an instrument, we're here to help.