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Genome Biol. 2011;12(3):R22. doi: 10.1186/gb-2011-12-3-r22. Epub 2011 Mar 16.

Improving RNA-Seq expression estimates by correcting for fragment bias.

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  • 1Department of Computer Science, 387 Soda Hall, UC Berkeley, Berkeley, CA 94720, USA.

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.

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