Improving RNA-Seq expression estimates by correcting for fragment bias
Adam Roberts, Cole Trapnell, Julie Donaghey, John L. Rinn, Lior Pachter
Abstract
The biochemistry of RNA-Seq library preparation results in cDNA fragments that are not uniformly distributed within the transcripts they represent. This non-uniformity must be accounted for when estimating expression levels, and we show how to perform the needed corrections using a likelihood based approach. We find improvements in expression estimates as measured by correlation with independently performed qRT-PCR and show that correction of bias leads to improved replicability of results across libraries and sequencing technologies.
Topics & Concepts
BiologyFragment (logic)RNA-SeqComputational biologyHuman geneticsGeneticsRNAEvolutionary biologyExpression (computer science)Genome BiologyGenomicsGene expressionTranscriptomeGenomeGeneComputer scienceAlgorithmProgramming languageRNA modifications and cancerCancer-related molecular mechanisms researchRNA Research and Splicing