An ultra-fast and scalable quantification pipeline for transposable elements from next generation sequencing data
An ultra-fast and scalable quantification pipeline for transposable elements from next generation sequencing data
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DOI：
10.1142/9789813235533_0016
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发表时间：
2018
影响因子：
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通讯作者：
Hyun-hwan Jeong;H. Yalamanchili;Caiwei Guo;J. Shulman;Zhandong Liu
中科院分区：
文献类型：
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作者：
Hyun-hwan Jeong;H. Yalamanchili;Caiwei Guo;J. Shulman;Zhandong Liu
转座元件 (TE) 是能够从一个位置移动到另一个位置的 DNA 序列，占人类基因组的很大一部分 (45%)。 TE 在癌症、神经退行性疾病和衰老等多种生物现象中发挥着重要作用。 RNA测序技术的快速发展使我们第一次能够在系统水平上研究TE的活性，但高效的TE分析工具尚未开发出来。在这项工作中，我们开发了 SalmonTE，这是一种快速可靠的管道，用于从 RNA-seq 数据中定量 TE。我们使用来自果蝇和人类细胞系的多个 RNA-seq 数据集，针对 TEtranscripts（一种广泛使用的 TE 量化方法）和其他三种量化方法对我们的工具进行了基准测试。我们在不影响准确性的情况下实现了 20 倍的执行速度。该管道将使生物医学研究界能够从大量数据中量化和分析 TE，并带来以 TE 为中心的新发现。
Transposable elements (TEs) are DNA sequences which are capable of moving from one location to another and represent a large proportion (45%) of the human genome. TEs have functional roles in a variety of biological phenomena such as cancer, neurodegenerative disease, and aging. Rapid development in RNA-sequencing technology has enabled us, for the first time, to study the activity of TE at the systems level.However, efficient TE analysis tools are not yet developed. In this work, we developed SalmonTE, a fast and reliable pipeline for the quantification of TEs from RNA-seq data. We benchmarked our tool against TEtranscripts, a widely used TE quantification method, and three other quantification methods using several RNA-seq datasets from Drosophila melanogaster and human cell-line. We achieved 20 times faster execution speed without compromising the accuracy. This pipeline will enable the biomedical research community to quantify and analyze TEs from large amounts of data and lead to novel TE centric discoveries.