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A pipeline for PAR-CLIP data analysis

Item Type:Article
Title:A pipeline for PAR-CLIP data analysis
Creators Name:Jens, M.
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.
Keywords:PAR-CLIP, CLIP, UV, Cross-Linking, Next-Generation Ssequencing, High-Throughput, Transcriptome, RNA, Small RNA, miRNA, mRNA, RNA-Binding Protein, RBP, Binding Site, FLEXBAR, Adapter Removal, Read Mapping, BWA, False-Positive Filtering, BWA PSSM, Consensus-Binding Sites
Source:Methods in Molecular Biology
Series Name:Methods in Molecular Biology
Title of Book:Post-Transcriptional Gene Regulation
ISSN:1064-3745
ISBN:978-1-4939-3066-1
Publisher:Springer / Humana Press (U.S.A.)
Volume:1358
Page Range:197-207
Number of Pages:353
Date:2016
Official Publication:https://doi.org/10.1007/978-1-4939-3067-8_12
PubMed:View item in PubMed

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