@inbook{2ba9050a682e4762813af824efe55fbe,
title = "Detecting Medium and Large Insertions and Deletions with transIndel",
abstract = "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.",
keywords = "Chimeric alignment, DNA-seq, Indel detection, RNA-seq, Split reads",
author = "Wang, {Ting You} and Rendong Yang",
note = "Publisher Copyright: {\textcopyright} 2022, The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.",
year = "2022",
doi = "10.1007/978-1-0716-2293-3_5",
language = "English (US)",
series = "Methods in Molecular Biology",
publisher = "Humana Press Inc.",
pages = "67--75",
booktitle = "Methods in Molecular Biology",
}