Improving RNA-Seq Expression Estimates by Correcting for Fragment Bias

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

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.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Bias
  • Gene Expression Profiling*
  • Gene Library
  • Humans
  • Quality Improvement
  • Reproducibility of Results
  • Sequence Analysis, RNA / methods*