iCLIP data analysis: A complete pipeline from sequencing reads to RBP binding sites.
Binding sites
Bioinformatics
Data processing
RNA-binding protein
UV crosslink events
iCLIP
Journal
Methods (San Diego, Calif.)
ISSN: 1095-9130
Titre abrégé: Methods
Pays: United States
ID NLM: 9426302
Informations de publication
Date de publication:
01 06 2020
01 06 2020
Historique:
received:
01
07
2019
revised:
13
11
2019
accepted:
14
11
2019
pubmed:
22
11
2019
medline:
8
6
2021
entrez:
22
11
2019
Statut:
ppublish
Résumé
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.
Identifiants
pubmed: 31751605
pii: S1046-2023(18)30494-8
doi: 10.1016/j.ymeth.2019.11.008
pii:
doi:
Substances chimiques
RNA
63231-63-0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
49-62Informations de copyright
Copyright © 2019 The Authors. Published by Elsevier Inc. All rights reserved.