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.
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| Author: | Anke BuschORCiD, Mirko BrüggemannORCiDGND, Stefanie EbersbergerORCiD, Katharina ZarnackORCiDGND |
|---|---|
| URN: | urn:nbn:de:hebis:30:3-535343 |
| DOI: | https://doi.org/10.1016/j.ymeth.2019.11.008 |
| ISSN: | 1095-9130 |
| ISSN: | 1046-2023 |
| Pubmed Id: | https://pubmed.ncbi.nlm.nih.gov/31751605 |
| Parent Title (English): | Methods |
| Publisher: | Academic Press |
| Place of publication: | Orlando, Fla. |
| Document Type: | Article |
| Language: | English |
| 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 |
| Volume: | 178 |
| Page Number: | 14 |
| First Page: | 49 |
| Last Page: | 62 |
| Note: | Under a Creative Commons license |
| HeBIS-PPN: | 46728976X |
| 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.) |
| Sammlungen: | Universitätspublikationen |
| Licence (German): |  Creative Commons - Namensnennung-Nicht kommerziell - Keine Bearbeitung 4.0 |
