MITIE: Simultaneous RNA-Seq-based transcript identification and quantification in multiple samples.

ABSTRACT:

Motivation

High-throughput sequencing of mRNA (RNA-Seq) has led to tremendous improvements in the detection of expressed genes and reconstruction of RNA transcripts. However, the extensive dynamic range of gene expression, technical limitations and biases, as well as the observed complexity of the transcriptional landscape, pose profound computational challenges for transcriptome reconstruction.

Results

We present the novel framework MITIE (Mixed Integer Transcript IdEntification) for simultaneous transcript reconstruction and quantification. We define a likelihood function based on the negative binomial distribution, use a regularization approach to select a few transcripts collectively explaining the observed read data and show how to find the optimal solution using Mixed

SUBMITTER: Behr J 

PROVIDER: S-EPMC3789545 | biostudies-literature | 2013 Oct

REPOSITORIES: biostudies-literature