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Nucleic Acids Res. 2018 Jan 25;46(2):e9. doi: 10.1093/nar/gkx1053.

Universal correction of enzymatic sequence bias reveals molecular signatures of protein/DNA interactions.

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1
Biochemistry and Molecular Genetics Department, University of Virginia, Charlottesville, Virginia, USA.
2
Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA.

Abstract

Coupling molecular biology to high-throughput sequencing has revolutionized the study of biology. Molecular genomics techniques are continually refined to provide higher resolution mapping of nucleic acid interactions and structure. Sequence preferences of enzymes can interfere with the accurate interpretation of these data. We developed seqOutBias to characterize enzymatic sequence bias from experimental data and scale individual sequence reads to correct intrinsic enzymatic sequence biases. SeqOutBias efficiently corrects DNase-seq, TACh-seq, ATAC-seq, MNase-seq and PRO-seq data. We show that seqOutBias correction facilitates identification of true molecular signatures resulting from transcription factors and RNA polymerase interacting with DNA.

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