Preparation of Non-overlapping Transposable Elements (TEs) Annotation by Interval Tree
Preparation of Non-overlapping Transposable Elements (TEs) Annotation by Interval Tree
复制标题
通过区间树准备不重叠的转座元素（TE）注释
DOI：
10.1007/978-1-0716-2380-0_21
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发表时间：
2022
影响因子：
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通讯作者：
Kojima Shohei
中科院分区：
文献类型：
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作者：
1.Kenji Tamura;Yuki Kanazashi;Chiaki Kawada;Yuya Sekine;Kazuhiro Maejima;Shingo Ashida;Takashi Karashima;Shohei Kojima;Nickolas F Parrish;Shunichi Kosugi;Chikashi Terao;Shota Sasagawa;Masashi Fujita;Todd A Johnson;Yukihide Momozawa;Keiji In;Kojima Shohei
转座元件(TES)是PIWI相互作用RNAs(PiRNAs)的主要来源，因此正确地将piRNA文库测序读数分配给TES，对于准确评估piRNA生物学具有重要意义。当计算映射到各种TE的小RNA序列读数的丰度时，非重叠TE注释是优选的，因为当计算读数时，映射到一个以上基因组特征的读数通常被排除在外。然而，大多数未经修改的TE注解在TE特征之间包含一定程度的重叠。在这里，我概述了原理，并提供了利用计算效率高的树算法将这些重叠区域的TE注释解析为单个最佳TE注释所需的所有脚本。该方法生成的非重叠标注可直接在常用的阅读统计软件中使用。
Transposable elements (TEs) are a major source of PIWI-interacting RNAs (piRNAs), therefore properly assigning piRNA library sequencing reads to the TEs from which they were derived is important for accurate assessment of piRNA biology. When calculating the abundance of small RNA-seq reads mapping to various TEs, a non-overlapping TE annotation is preferable because reads mapping to more than one genomic feature will often be excluded when counting reads. However, most unmodified TE annotations contain some degree of overlap between TE features. Here, I outline the principle and provide all scripts needed to resolve such overlapping regions of TE annotations to a single best TE annotation leveraging a computationally efficient tree algorithm. Non-overlapping annotations generated by this method can be directly used in commonly used read counting software.