iCLIP data analysis: A complete pipeline from sequencing reads to RBP binding sites
iCLIP data analysis: A complete pipeline from sequencing reads to RBP binding sites
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DOI：
10.1016/j.ymeth.2019.11.008
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发表时间：
2020-06-01
期刊：
影响因子：
4.8
通讯作者：
Zarnack, Kathi
中科院分区：
文献类型：
--
作者：
Busch, Anke;Brueggemann, Mirko;Zarnack, Kathi
准确了解RNA结合蛋白(RBP)的结合位点是理解基因表达复杂的转录后调控的关键。这些信息可以通过单核苷酸拆分、紫外光交联和免疫沉淀(ICLIP)实验获得。在这里，我们提供了一个完整的数据分析工作流程，以可靠地从iCLIP数据中检测RBP结合位点。该工作流程涵盖了从测序读物的初始质量控制到RBP结合的峰值调用和量化的所有步骤。对于每个工具，我们解释了iCLIP数据分析的具体要求，并建议优化参数设置。
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.