iCLIP data analysis: A complete pipeline from sequencing reads to RBP binding sites

  • Precise knowledge on the binding sites of an RNA-binding protein (RBP) is key to understanding the complex post-transcriptional regulation of gene expression. This information can be obtained from individual-nucleotide resolution UV crosslinking and immunoprecipitation (iCLIP) experiments. Here, we present a complete data analysis workflow to reliably detect RBP binding sites from iCLIP data. The workflow covers all steps from the initial quality control of the sequencing reads up to peak calling and quantification of RBP binding. For each tool, we explain the specific requirements for iCLIP data analysis and suggest optimised parameter settings.
Author:Anke BuschORCiD, Mirko BrüggemannORCiDGND, Stefanie EbersbergerORCiD, Katharina ZarnackORCiDGND
Pubmed Id:https://pubmed.ncbi.nlm.nih.gov/31751605
Parent Title (English):Methods
Publisher:Academic Press
Place of publication:Orlando, Fla.
Document Type:Article
Year of Completion:2019
Date of first Publication:2019/11/18
Publishing Institution:Universitätsbibliothek Johann Christian Senckenberg
Release Date:2020/06/10
Tag:RNA-binding protein; UV crosslink events; binding sites; bioinformatics; data processing; iCLIP
Page Number:14
First Page:49
Last Page:62
Under a Creative Commons license
Institutes:Biowissenschaften / Biowissenschaften
Exzellenzcluster / Exzellenzcluster Makromolekulare Komplexe
Dewey Decimal Classification:5 Naturwissenschaften und Mathematik / 57 Biowissenschaften; Biologie / 570 Biowissenschaften; Biologie
MSC-Classification:00-XX GENERAL / 00-01 Instructional exposition (textbooks, tutorial papers, etc.)
Licence (German):License LogoCreative Commons - Namensnennung-Nicht kommerziell - Keine Bearbeitung 4.0