期刊
METHODS
卷 178, 期 -, 页码 96-103出版社
ACADEMIC PRESS INC ELSEVIER SCIENCE
DOI: 10.1016/j.ymeth.2019.09.020
关键词
icSHAPE; RNA secondary structure; icSHAPE reactivity/structure score
资金
- Chinese Ministry of Science and Technology [2018YFA0107603]
- National Natural Science Foundation of China [91740204, 31761163007, 31621063]
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.
作者
我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。
推荐
暂无数据