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

The Hormel Institute

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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
Volume	2493
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
RNA Splicing
Algorithms
DNA
Software
INDEL Mutation

PubMed: MeSH publication types

Journal Article

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

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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.",

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T1 - Detecting Medium and Large Insertions and Deletions with transIndel

AU - Wang, Ting You

AU - Yang, Rendong

PY - 2022

Y1 - 2022

N2 - 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.

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.

KW - Chimeric alignment

KW - DNA-seq

KW - Indel detection

KW - RNA-seq

KW - Split reads

KW - RNA Splicing

KW - Algorithms

KW - DNA

KW - Software

KW - INDEL Mutation

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M3 - Chapter

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AN - SCOPUS:85133101702

VL - 2493

T3 - Methods in Molecular Biology

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BT - Methods in Molecular Biology

PB - Humana Press Inc.

ER -

Detecting Medium and Large Insertions and Deletions with transIndel

Abstract

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