title: A Pipeline for PAR-CLIP Data Analysis.
abstract: Photo-activatable ribonucleoside cross-linking and immunoprecipitation (PAR-CLIP) is a method to detect binding sites of RNA-binding proteins (RBPs) transcriptome-wide. This chapter covers the computational analysis of the high-throughput sequencing reads generated from PAR-CLIP experiments. It explains how the reads are mutated due to UV cross-linking and how to appropriately pre-process and align them to a reference sequence. Aligned reads are then aggregated into clusters which represent putative RBP-binding sites. Mapping artifacts are a source of false positives, which can be controlled by means of a mapping decoy and adaptive quality filtering of the read clusters. A step-by-step explanation of this procedure is given. All necessary tools are open source, including the scripts presented and used in this chapter.
authors.affiliation: Systems Biology of Gene Regulatory Elements, Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany. marvin.jens@mdc-berlin.de.
authors.forename: Marvin
authors.initials: M
authors.lastname: Jens
mesh_terms: D001665:Binding Sites / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D047468:Immunoprecipitation; D012313:RNA / Q000235:genetics*; D016601:RNA-Binding Proteins / Q000235:genetics*; D059467:Transcriptome / Q000235:genetics*
chemical_list: D016601:RNA-Binding Proteins; D012313:RNA
keywords: Adapter removal; BWA; BWA PSSM; Binding site; CLIP; Consensus-binding sites; Cross-linking; FLEXBAR; False-positive filtering; High-throughput; Next-generation sequencing; PAR-CLIP; RBP; RNA; RNA-binding protein; Read mapping; Small RNA; Transcriptome; UV; mRNA; miRNA