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

Authors
  • Busch, Anke1
  • Brüggemann, Mirko2
  • Ebersberger, Stefanie3
  • Zarnack, Kathi4
  • 1 Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany. , (Germany)
  • 2 Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt, Germany. , (Germany)
  • 3 Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany. Electronic address: [email protected] , (Germany)
  • 4 Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt, Germany. Electronic address: [email protected] , (Germany)
Type
Published Article
Journal
Methods
Publisher
Elsevier
Publication Date
Jun 01, 2020
Volume
178
Pages
49–62
Identifiers
DOI: 10.1016/j.ymeth.2019.11.008
PMID: 31751605
Source
Medline
Keywords
Language
English
License
Unknown

Abstract

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. Copyright © 2019 The Authors. Published by Elsevier Inc. All rights reserved.

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