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.
CITATION STYLE
Wang, T. Y., & Yang, R. (2022). Detecting Medium and Large Insertions and Deletions with transIndel. In Methods in Molecular Biology (Vol. 2493, pp. 67–75). Humana Press Inc. https://doi.org/10.1007/978-1-0716-2293-3_5
Mendeley helps you to discover research relevant for your work.