摘要
RNA编辑是重要的转录后修饰过程,目前已有多种算法用于识别RNA编辑,本文主要研究小鼠中测序深度对RNA编辑识别算法的影响,从而为RNA编辑的研究给出建议的方法.本文使用STAR比对软件将小鼠的RNA-seq数据进行序列比对,然后使用GATK识别SNV,并用Separate Method、GIREMI、RNAEditor 3种方法识别出RNA编辑位点.最后对3种方法识别RNA编辑位点的共同部分、识别效率、识别稳定性、识别与测序深度的关系进行分析.结果发现3种方法识别的编辑位点数目差异大,共有位点较少,随着测序深度的增加,识别的RNA编辑位点数也在增加.结果表明RNA编辑识别算法在小鼠中的识别性能与测序深度呈正相关.
RNA editing is an important post-transcriptional modification process. There are many algorithms used to identify RNA editing. This study of the sequencing depth’s effect on RNA editing will provide a suggested method for RNA editing research. Mouse reference genome was mapped to the RNA-seq by STAR. Then identified SNV by GATK, finally RNA Editing sites were filtered by Separate method, GIREMI and RNAEditor.The results showed the identification of RNA editing varied in three methods. There was little overlap in results.As the sequencing depth increases, the identified number of RNA editing sites also increases. In conclusion, the identification of RNA editing sites is positive correlated with the sequencing depth.
作者
赵诚辉
洪浩
李宛莹
李睿江
江帅
李昊
陈河兵
伯晓晨
ZHAO Cheng-Hui;HONG Hao;LI Wan-Ying;LI Rui-Jiang;JIANG Shuai;LI Hao;CHEN He-Bing;BO Xiao-Chen(Institute of Radiation Medicine,Academy of Military Medical Sciences,Beijing 100850,China)
出处
《生物化学与生物物理进展》
SCIE
CAS
CSCD
北大核心
2019年第12期1202-1208,共7页
Progress In Biochemistry and Biophysics
基金
国家自然科学基金重点项目(U1435222)资助~~
