Detecting Medium and Large Insertions and Deletions with transIndel

Ting You Wang, Rendong Yang*

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingChapter


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 languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Number of pages9
StatePublished - 2022

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029


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

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics


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