A pipeline for PAR-CLIP data analysis

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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
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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