Piecing the puzzle together: a revisit to transcript reconstruction problem in RNA-seq.

ABSTRACT: The advancement of RNA sequencing (RNA-seq) has provided an unprecedented opportunity to assess both the diversity and quantity of transcript isoforms in an mRNA transcriptome. In this paper, we revisit the computational problem of transcript reconstruction and quantification. Unlike existing methods which focus on how to explain the exons and splice variants detected by the reads with a set of isoforms, we aim at reconstructing transcripts by piecing the reads into individual effective transcript copies. Simultaneously, the quantity of each isoform is explicitly measured by the number of assembled effective copies, instead of estimated solely based on the collective read count. We have developed a novel method named Astroid that solves the problem of effective copy reconstruction on the b

SUBMITTER: Huang Y 

PROVIDER: S-EPMC4168703 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature