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Roberts, Adam; Trapnell, Cole; Donaghey, Julie; Rinn, John L; Pachter, Lior
Genome biology, 03/2011, Volume: 12, Issue: 3Journal Article
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.
