Apr 8, 2020

Terminus enables the discovery of data-driven, robust transcript groups from RNA-seq data

BioRxiv : the Preprint Server for Biology
H. SarkarRob Patro

Abstract

Motivation: Advances in sequencing technology, inference algorithms and differential testing methodology have enabled transcript-level analysis of RNA-seq data. Yet, the inherent inferential uncertainty in transcript-level abundance estimation, even among the most accurate approaches, means that robust transcript-level analysis often remains a challenge. Conversely, gene-level analysis remains a common and robust approach for understanding RNA-seq data, but it coarsens the resulting analysis to the level of genes, even if the data strongly support specific transcript-level effects. Results: We introduce a new data-driven approach for grouping together transcripts in an experiment based on their inferential uncertainty. Transcripts that share large numbers of ambiguously-mapping fragments with other transcripts, in complex patterns, often cannot have their abundances confidently estimated. Yet, the total transcriptional output of that group of transcripts will have greatly-reduced inferential uncertainty, thus allowing more robust and confident downstream analysis. Our approach, implemented in the tool terminus, groups together transcripts in a data-driven manner allowing transcript-level analysis where it can be confidently sup...Continue Reading

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Mentioned in this Paper

Bacterial cell
Physiologic Pulse
Bacteriophages
Recombination, Genetic
Medical Devices
Cell Differentiation Process
Integrase Activity
Monitoring - Action
Cell-mediated Immune Response
Chemicals

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