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Protocol for generating customizable and reproducible plots of sequencing coverage data using the seqNdisplayR package.

ABSTRACT: The widespread usage of next-generation sequencing methods for functional genomics studies requires standardized tools for consistent visualization of the associated data. Here, we present seqNdisplayR, an R package for plotting standard sequencing data coverage within a genomic region of interest in a customizable and reproducible manner. We describe steps for installing software, preparing data files, choosing options, and plotting data. This tool is readily available for users with no prior experience with R through the "Shiny app" interface. For complete details on the use and execution of this protocol, please refer to Lykke-Andersen et al.,¹ Gockert et al.,² and Rouviere et al.³.

SUBMITTER: Lykke-Andersen S

PROVIDER: S-EPMC10963655 | biostudies-literature | 2024 Mar

REPOSITORIES: biostudies-literature

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Protocol for generating customizable and reproducible plots of sequencing coverage data using the seqNdisplayR package.

Lykke-Andersen Søren S Rouvière Jérôme O JO Schmid Manfred M Gockert Maria M Jensen Torben Heick TH

STAR protocols 20240318 2

The widespread usage of next-generation sequencing methods for functional genomics studies requires standardized tools for consistent visualization of the associated data. Here, we present seqNdisplayR, an R package for plotting standard sequencing data coverage within a genomic region of interest in a customizable and reproducible manner. We describe steps for installing software, preparing data files, choosing options, and plotting data. This tool is readily available for users with no prior e ...[more]

PMID: 38502686

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Dataset Information

Protocol for generating customizable and reproducible plots of sequencing coverage data using the seqNdisplayR package.

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Protocol for generating customizable and reproducible plots of sequencing coverage data using the seqNdisplayR package.

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