iCLIP data analysis: A complete pipeline from sequencing reads to RBP binding sites.
Methods
; 178: 49-62, 2020 06 01.
Article
de En
| MEDLINE
| ID: mdl-31751605
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.
Mots clés
Texte intégral:
1
Collection:
01-internacional
Base de données:
MEDLINE
Sujet principal:
ARN
/
Immunoprécipitation
/
Séquençage nucléotidique à haut débit
Limites:
Humans
Langue:
En
Journal:
Methods
Sujet du journal:
BIOQUIMICA
Année:
2020
Type de document:
Article
Pays d'affiliation:
Allemagne