SUPPA2: fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditions.
SUPPA2: fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditions.
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DOI：
10.1186/s13059-018-1417-1
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发表时间：
2018-03-23
期刊：
影响因子：
12.3
通讯作者：
Eyras E
中科院分区：
文献类型：
--
作者：
Trincado JL;Entizne JC;Hysenaj G;Singh B;Skalic M;Elliott DJ;Eyras E
尽管研究 RNA-seq 差异剪接的方法有很多，但许多挑战仍未解决，包括计算能力和测序深度要求。在这里，我们提出了 SUPPA2，这是一种解决这些挑战的新方法，并能够在考虑生物变异性的情况下跨多种条件进行简化分析。使用实验和模拟数据，我们表明 SUPPA2 与其他方法相比具有更高的准确性，特别是在低测序深度和短读长的情况下。我们使用 SUPPA2 来识别新的 Transformer2 调节的外显子、双极神经元分化过程中诱导的新的微外显子以及成红细胞分化过程中的新的内含子保留事件。本文的在线版本 (10.1186/s13059-018-1417-1) 包含补充材料，可供授权用户使用。
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. The online version of this article (10.1186/s13059-018-1417-1) contains supplementary material, which is available to authorized users.
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