环状RNA
计算生物学
计算机科学
深度测序
RNA剪接
核糖核酸
RNA序列
基因亚型
生物
基因
遗传学
转录组
基因表达
基因组
作者
Guoxia Wen,Musheng Li,Fuyu Li,Zengyan Yang,Tong Zhou,Wanjun Gu
出处
期刊:Bioinformatics
[Oxford University Press]
日期:2021-06-11
卷期号:37 (24): 4879-4881
被引量:2
标识
DOI:10.1093/bioinformatics/btab435
摘要
ABSTRACT Summary Currently, most computational methods estimate the expression of circular RNAs (circRNAs) using the number of sequencing reads that support back–splicing junctions (BSJ) in RNA-seq data, which may introduce biased estimation of circRNA expression due to the uneven distribution of sequencing reads. To overcome this, we previously developed a model-based strategy for circRNA quantification, enabling consideration of sequencing reads from the entire transcript. Yet, the lack of exact transcript structure of circRNAs may limit its accuracy. Here, we proposed a substantially improved circRNA quantification tool, AQUARIUM, by introducing the full-length RNA structure of circular isoforms. We assessed its performance in circRNA quantification using both biological and simulated rRNA-depleted RNA-seq datasets, and demonstrated its superior performance at both BSJ and isoform level. Availability and implementation AQUARIUM is freely available at https://github.com/wanjun-group-seu/AQUARIUM. Supplementary information Supplementary data are available at Bioinformatics online.
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