Detecting Medium and Large Insertions and Deletions with transIndel

Ting You Wang; Rendong Yang

doi:10.1007/978-1-0716-2293-3_5

Detecting Medium and Large Insertions and Deletions with transIndel

Ting You Wang, Rendong Yang

Hormel Institute

Research output: Chapter in Book/Report/Conference proceeding › Chapter

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.

Original language	English (US)
Title of host publication	Methods in Molecular Biology
Publisher	Humana Press Inc.
Pages	67-75
Number of pages	9
DOIs	https://doi.org/10.1007/978-1-0716-2293-3_5
State	Published - 2022

Publication series

Name	Methods in Molecular Biology
Volume	2493
ISSN (Print)	1064-3745
ISSN (Electronic)	1940-6029

Bibliographical note

Publisher Copyright:
© 2022, The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.

Keywords

Chimeric alignment
DNA-seq
Indel detection
RNA-seq
Split reads

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AU - Yang, Rendong

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AB - 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.

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KW - DNA-seq

KW - Indel detection

KW - RNA-seq

KW - Split reads

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Detecting Medium and Large Insertions and Deletions with transIndel

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