生物
RNA剪接
计算生物学
外显子
内含子
差速器(机械装置)
人类遗传学
选择性拼接
RNA序列
DNA测序
深度测序
遗传学
核糖核酸
基因
转录组
基因组
基因表达
工程类
航空航天工程
作者
Juan L. Trincado,Juan Carlos Entizne,Gerald Hysenaj,Babita Singh,Miha Škalič,David Elliott,Eduardo Eyras
出处
期刊:Genome Biology
[Springer Nature]
日期:2018-03-23
卷期号:19 (1)
被引量:369
标识
DOI:10.1186/s13059-018-1417-1
摘要
Despite the many approaches to study differential splicing from RNA-seq, many challenges remain unsolved, including computing capacity and sequencing depth requirements. Here we present SUPPA2, a new method that addresses these challenges, and enables streamlined analysis across multiple conditions taking into account biological variability. Using experimental and simulated data, we show that SUPPA2 achieves higher accuracy compared to other methods, especially at low sequencing depth and short read length. We use SUPPA2 to identify novel Transformer2-regulated exons, novel microexons induced during differentiation of bipolar neurons, and novel intron retention events during erythroblast differentiation.
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