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icSHAPE-pipe: A comprehensive toolkit for icSHAPE data analysis and evaluation.

Authors
  • Li, Pan1
  • Shi, Ruoyao2
  • Zhang, Qiangfeng Cliff3
  • 1 MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology, Center for Synthetic and Systems Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China. Electronic address: [email protected] , (China)
  • 2 BioKnow Health Informatics Lab, College of Life Science, Jilin University, Changchun 130012, China. Electronic address: [email protected] , (China)
  • 3 MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology, Center for Synthetic and Systems Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China. Electronic address: [email protected] , (China)
Type
Published Article
Journal
Methods
Publisher
Elsevier
Publication Date
Jun 01, 2020
Volume
178
Pages
96–103
Identifiers
DOI: 10.1016/j.ymeth.2019.09.020
PMID: 31606387
Source
Medline
Keywords
Language
English
License
Unknown

Abstract

RNA molecules have the intrinsic ability to fold into complex structures that are important in regulating many biological processes, including transcription, translation, processing and degradation. However, our knowledge for RNA structures remains very limited. Previously, we developed icSHAPE, a high-throughput method to probe single-stranded RNA nucleotide in cells. To recover the structural profile of an RNA or a transcript by icSHAPE, it is essential to accurately calculate an icSHAPE reactivity as the RNA structure score for each base. Here, we present icSHAPE-pipe, a comprehensive toolkit for the analysis of RNA structure sequencing data obtained from icSHAPE experiments. Compared to the original icSHAPE data processing protocol, icSHAPE-pipe calculates RNA structural information with higher accuracy and achieves higher coverage of the transcriptome. In addition, icSHAPE-pipe can perform quality control, and generate reports on sequencing data and the statistics of results. In sum, icSHAPE-pipe provides a convenient workflow for researchers to analyze RNA structural data from icSHAPE sequencing experiments. Copyright © 2019 Elsevier Inc. All rights reserved.

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