title: Improving RNA-Seq expression estimates by correcting for fragment bias.
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.
authors.affiliation: Department of Computer Science, 387 Soda Hall, UC Berkeley, Berkeley, CA 94720, USA.
authors.forename: Adam
authors.initials: A
authors.lastname: Roberts
authors.forename: Cole
authors.initials: C
authors.lastname: Trapnell
authors.forename: Julie
authors.initials: J
authors.lastname: Donaghey
authors.forename: John L
authors.initials: JL
authors.lastname: Rinn
authors.forename: Lior
authors.initials: L
authors.lastname: Pachter
mesh_terms: D015982:Bias; D020869:Gene Expression Profiling; D015723:Gene Library; D006801:Humans; D058996:Quality Improvement; D015203:Reproducibility of Results; D017423:Sequence Analysis, RNA / Q000379:methods*