PT - JOURNAL ARTICLE AU - Yaron Orenstein AU - Raghavendra Hosur AU - Sean Simmons AU - Jadwiga Bienkoswka AU - Bonnie Berger TI - Sequence biases in CLIP experimental data are incorporated in protein RNA-binding models AID - 10.1101/075259 DP - 2016 Jan 01 TA - bioRxiv PG - 075259 4099 - http://biorxiv.org/content/early/2016/09/14/075259.short 4100 - http://biorxiv.org/content/early/2016/09/14/075259.full AB - 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 [1], 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.