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

Jonas Behr, André Kahles, Yi Zhong, Vipin T. Sreedharan, Philipp Drewe, Gunnar Rätsch

Abstract: 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.