TY  - JOUR
A1  - Busch, Anke
A1  - Brüggemann, Mirko
A1  - Ebersberger, Stefanie
A1  - Zarnack, Katharina
T1  - iCLIP data analysis: A complete pipeline from sequencing reads to RBP binding sites
T2  - Methods
N2  - 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.
KW  - iCLIP
KW  - bioinformatics
KW  - data processing
KW  - UV crosslink events
KW  - binding sites
KW  - RNA-binding protein
Y1  - 2019
UR  - http://publikationen.ub.uni-frankfurt.de/frontdoor/index/index/docId/53534
UR  - https://nbn-resolving.org/urn:nbn:de:hebis:30:3-535343
SN  - 1095-9130
SN  - 1046-2023
N1  - Under a Creative Commons license
VL  - 178
SP  - 49
EP  - 62
PB  - Academic Press
CY  - Orlando, Fla.
ER  -