Improving RNA-Seq expression estimates by correcting for fragment bias

Adam Roberts, Cole Trapnell, Julie Donaghey, John L. Rinn, Lior Pachter. 2011.
Genome Biology 12:R22.

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.