The Hormel Institute, University of Minnesota, Austin, MN, USA.
Methods Mol Biol. 2022;2493:67-75. doi: 10.1007/978-1-0716-2293-3_5.
Insertions and deletions (indels) are primarily detected from DNA sequencing (DNA-seq) data, but their transcriptional consequences remain unexplored due to challenges in distinguishing medium- and large-sized indels from RNA splicing events in RNA-seq data. We introduce transIndel, a splice-aware algorithm that parses the chimeric alignments predicted by a short read aligner and reconstructs the mid-sized insertions and large deletions based on the linear alignments of split reads from DNA-seq or RNA-seq data. Here, we describe the method and provide a tutorial on the installation and application of transIndel.
插入和缺失（indels）主要是从 DNA 测序（DNA-seq）数据中检测到的，但由于在 RNA-seq 数据中区分中等大小和大的 indels 与 RNA 剪接事件的挑战，它们的转录后果仍未被探索。我们引入了 transIndel，这是一种拼接感知算法，它解析由短读对齐器预测的嵌合比对，并根据来自 DNA-seq 或 RNA-seq 数据的拆分读取的线性比对来重建中型插入和大缺失。在这里，我们描述了该方法，并提供了关于 transIndel 的安装和应用的教程。
