article Open AccessTop 1% cited
Improving RNA-Seq expression estimates by correcting for fragment bias
Genome biology · 2011 · Vol. 12(3) · pp. R22–R22
Adam Roberts(Berkeley College)Cole Trapnell(Harvard University)Julie Donaghey(Broad Institute)John L. Rinn(Harvard University)Lior Pachter✉(University of California, Berkeley)
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.
RNA modifications and cancerCancer-related molecular mechanisms researchRNA Research and SplicingBiologyFragment (logic)RNA-SeqComputational biologyHuman geneticsGeneticsRNAEvolutionary biologyExpression (computer science)Genome Biology
MeSH terms
HumansReproducibility of ResultsGene LibraryBiasSequence Analysis, RNAGene Expression ProfilingQuality Improvement
Funding
- National Science Foundation
Citations
1,812
FWCI
39.39
field-weighted impact
References
33
Percentile
100%
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Citations per year
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References
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Genome biology · 2009 · 22,766 citations
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