MiClip: A Model-based Approach to Identify Binding Sites in CLIP-Seq Data

Cross-linking immunoprecipitation coupled with high-throughput sequencing (CLIP-Seq) has made it possible to identify targeting sites of RNA-binding proteins in various cell culture systems and tissue types on a genome-wide scale. Here we present MiClip,a novel model-based approach to identify high-confidence protein-RNA binding sites in CLIP-Seq datasets. This approach assigns confidence value to each binding site on a probabilistic basis. The MiClip package can be flexibly applied to analyze both HITS-CLIP data and PAR-CLIP data.

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