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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.

SUBMITTER: Roberts A 

PROVIDER: S-EPMC3129672 | biostudies-literature | 2011

REPOSITORIES: biostudies-literature

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

Roberts Adam A   Trapnell Cole C   Donaghey Julie J   Rinn John L JL   Pachter Lior L  

Genome biology 20110316 3

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 acros  ...[more]