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Sequence biases in CLIP experimental data are incorporated in protein RNA-binding models

By Yaron Orenstein, Raghavendra Hosur, Sean Simmons, Jadwiga Bienkoswka, Bonnie Berger

Posted 14 Sep 2016
bioRxiv DOI: 10.1101/075259

We report a newly-identified bias in CLIP data that results from cleaving enzyme specificity. This bias is inadvertently incorporated into standard peak calling methods, which identify the most likely locations where proteins bind RNA. We further show how, in downstream analysis, this bias is incorporated into models inferred by the state-of-the-art GraphProt method to predict protein RNA-binding. We call for both experimental controls to measure enzyme specificities and algorithms to identify unbiased CLIP binding sites.

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