Library generation introduces significant biases in RNA-seq data, adding extreme variability to coverage and read-depth

RNA-seq is a powerful technique for identifying and quantifying transcription and splicing events, both known and novel. However, given its recent development and the proliferation of library construction methods, understanding the bias it introduces is incomplete but critical to realizing its value.

Researchers at the University of Pennsylvania present a method, in vitro transcription sequencing (IVT-seq), for identifying and assessing the technical biases in RNA-seq library generation and sequencing at scale. They created a pool of over 1000 in vitro transcribed (IVT) RNAs from a full-length human cDNA library and sequenced them with polyA and total RNA-seq, the most common protocols. Because each cDNA is full length, and they show IVT is incredibly processive, each base in each transcript should be equivalently represented. However, with common RNA-seq applications and platforms, the researchers found 50% of transcripts have more than 2-fold and 10% have more than 10-fold differences in within-transcript sequence coverage. They also found greater than 6% of transcripts have regions of dramatically unpredictable sequencing coverage between samples, confounding accurate determination of their expression. The researchers use a combination of experimental and computational approaches to show rRNA depletion is responsible for the most significant variability in coverage, and several sequence determinants also strongly influence representation.


These results show the utility of IVT-seq for promoting better understanding of bias introduced by RNA-seq. The researches found rRNA depletion is responsible for substantial, unappreciated biases in coverage introduced during library preparation. These biases suggest exon-level expression analysis may be inadvisable, and we recommend caution when interpreting RNA-seq results.

Lahens NF, Kavakli IH, Zhang R, Hayer K, Black MB, Dueck H, Pizarro A, Kim J, Irizarry R, Thomas RS, Grant GR, Hogenesch JB. (2014) IVT-seq reveals extreme bias in RNA-sequencing. Genome Biology 15, R86. [abstract]